BFO_0000050
RO_0040042: BFO_0000002
RO_0040042: BFO_0000003
RO_0040042: BFO_0000004
RO_0040042: BFO_0000017
RO_0040042: BFO_0000019
RO_0040042: BFO_0000020
RO_0040042: BFO_0000031
has db xref: BFO:0000050
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam
shorthand: part_of
type: ObjectProperty
sub property of: overlaps

BFO_0000051
has db xref: BFO:0000051
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_part
type: ObjectProperty
sub property of: overlaps

BFO_0000062
has db xref: BFO:0000062
in subset: ro-eco
shorthand: preceded_by
type: ObjectProperty

BFO_0000063
has db xref: BFO:0000063
in subset: ro-eco
shorthand: precedes
type: ObjectProperty
sub property of: RO_0002222

RO_0000053
has db xref: RO:0000053
shorthand: has_characteristic
type: ObjectProperty

RO_0000056
has db xref: RO:0000056
shorthand: participates_in
type: ObjectProperty

RO_0000057
has db xref: RO:0000057
shorthand: has_participant
type: ObjectProperty

is allergic trigger for
IAO_0000112: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
IAO_0000115: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has db xref: RO:0001020
shorthand: is_allergic_trigger_for
type: ObjectProperty
domain: BFO_0000040
sub property of: causes or contributes to condition
inverse of: has allergic trigger

is autoimmune trigger for
IAO_0000115: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has db xref: RO:0001021
shorthand: is_autoimmune_trigger_for
type: ObjectProperty
domain: BFO_0000040
sub property of: causes or contributes to condition
inverse of: has autoimmune trigger

has allergic trigger
IAO_0000112: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
IAO_0000115: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has db xref: RO:0001022
shorthand: has_allergic_trigger
type: ObjectProperty
range: BFO_0000040
sub property of: causes or contributes to condition

has autoimmune trigger
IAO_0000115: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has db xref: RO:0001023
shorthand: has_autoimmune_trigger
type: ObjectProperty
range: BFO_0000040
sub property of: causes or contributes to condition

RO_0002000
has db xref: RO:0002000
shorthand: 2D_boundary_of
type: ObjectProperty
sub property of: mereotopologically related to

RO_0002002
IAO_0000117: David Osumi-Sutherland
has db xref: RO:0002002
shorthand: has_2D_boundary
type: ObjectProperty
sub property of: mereotopologically related to

electrically_synapsed_to
IAO_0000115: A relation that holds between two neurons that are electrically coupled via gap junctions.
IAO_0000117: David Osumi-Sutherland
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002003
shorthand: electrically_synapsed_to
type: ObjectProperty
sub property of: connected to

innervated_by
IAO_0000117: David Osumi-Sutherland
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002005
shorthand: innervated_by
type: ObjectProperty
domain: CARO_0000003
range: CARO_0001001
inverse of: innervates

has synaptic terminal of
IAO_0000117: David Osumi-Sutherland
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002006
shorthand: has_synaptic_terminal_of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in

bounding layer of
IAO_0000115: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
IAO_0000117: David Osumi-Sutherland
has db xref: RO:0002007
in subset: ro-eco
shorthand: bounding_layer_of
type: ObjectProperty
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
domain: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002124
range: BFO_0000040
sub property of: BFO_0000050

coincident with
IAO_0000115: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: David Osumi-Sutherland
has db xref: RO:0002008
in subset: ro-eco
shorthand: coincident_with
type: ObjectProperty
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
domain: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001199
range: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001199
sub property of: mereotopologically related to

regulates in other organism
IAO_0000115: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
IAO_0000117: David Osumi-Sutherland
has db xref: RO:0002010
shorthand: regulates_in_other_organism
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000015
sub property of: causally upstream of or within

occurent part of
IAO_0000115: A part of relation that applies only between occurents.
has db xref: RO:0002012
shorthand: occurent_part_of
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000003
sub property of: BFO_0000050
sub property of: causally upstream of or within

has regulatory component activity
IAO_0000115: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z
has db xref: RO:0002013
shorthand: has_regulatory_component_activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by

has negative regulatory component activity
IAO_0000115: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:01Z
has db xref: RO:0002014
shorthand: has_negative_regulatory_component_activity
type: ObjectProperty
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
sub property of: has regulatory component activity
sub property of: negatively regulated by

has positive regulatory component activity
IAO_0000115: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
has db xref: RO:0002015
shorthand: has_positive_regulatory_component_activity
type: ObjectProperty
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
sub property of: has regulatory component activity
sub property of: positively regulated by

has necessary component activity
created by: dos
creation date: 2017-05-24T09:36:08Z
has db xref: RO:0002016
shorthand: has_necessary_component_activity
type: ObjectProperty
comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
sub property of: has component activity
sub property of: positively regulated by

has component activity
created by: dos
creation date: 2017-05-24T09:44:33Z
has db xref: RO:0002017
shorthand: has_component_activity
type: ObjectProperty
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
sub property of: has component process

has component process
IAO_0000115: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: dos
creation date: 2017-05-24T09:49:21Z
has db xref: RO:0002018
shorthand: has_component_process
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000015
sub property of: has component

has ligand
IAO_0000115: A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
created by: dos
creation date: 2017-07-19T17:30:36Z
has db xref: RO:0002019
shorthand: has_ligand
type: ObjectProperty
sub property of: has input

transports
IAO_0000115: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
created by: dos
creation date: 2017-07-20T17:11:08Z
has db xref: RO:0002020
shorthand: transports
type: ObjectProperty
sub property of: transports or maintains localization of

occurs across
IAO_0000115: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
created by: dos
creation date: 2017-07-20T17:19:37Z
has db xref: RO:0002021
shorthand: occurs_across
type: ObjectProperty
sub property of: has part that occurs in

directly regulated by
created by: dos
creation date: 2017-09-17T13:52:24Z
has db xref: RO:0002022
shorthand: directly_regulated_by
type: ObjectProperty
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
sub property of: regulated by
inverse of: directly regulates

directly negatively regulated by
IAO_0000115: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z
has db xref: RO:0002023
shorthand: directly_negatively_regulated_by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates

directly positively regulated by
IAO_0000115: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z
has db xref: RO:0002024
shorthand: directly_positively_regulated_by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates

has effector activity
IAO_0000115: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
has db xref: RO:0002025
shorthand: has_effector_activity
type: FunctionalProperty
type: ObjectProperty
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
sub property of: has component activity

in register with
IAO_0000115: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
created by: dos
creation date: 2017-12-07T12:58:06Z
has db xref: RO:0002026
shorthand: in_register_with
type: ObjectProperty
domain: image
range: image
sub property of: mereotopologically related to

RO_0002087
has db xref: RO:0002087
shorthand: immediately_preceded_by
type: ObjectProperty

RO_0002090
IAO_0000117: David Osumi-Sutherland
RO_0002575: BFO_0000063
has db xref: RO:0002090
in subset: ro-eco
shorthand: immediately_precedes
type: ObjectProperty

has soma location
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and an anatomical structure that its soma is part of.
IAO_0000117: David Osumi-Sutherland
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)
RO_0001900: RO_0001901
has db xref: RO:0002100
shorthand: has_soma_location
type: ObjectProperty
domain: CL_0000540
range: CARO_0000003
sub property of: overlaps

fasciculates with
IAO_0000114: IAO_0000125
IAO_0000115: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: fasciculates with
IAO_0000426: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002101
shorthand: fasciculates_with
type: ObjectProperty
domain: CL_0000540
range: CARO_0001001
sub property of: overlaps
inverse of: has fasciculating neuron projection

axon synapses in
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure its axon forms (chemical) synapses in.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
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)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002102
shorthand: axon_synapses_in
type: ObjectProperty
domain: CL_0000540
sub property of: has presynaptic terminal in

synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
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?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002103
shorthand: synapsed_by
type: ObjectProperty
range: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
sub property of: receives input from
inverse of: synapsed to

has plasma membrane part
IAO_0000112: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
IAO_0000114: IAO_0000125
IAO_0000115: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
IAO_0000117: Alexander Diehl
IAO_0000117: Chris Mungall
IAO_0000117: Lindsay Cowell
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19243617
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)
RO_0001900: RO_0001901
has db xref: RO:0002104
shorthand: has_plasma_membrane_part
type: ObjectProperty
domain: CARO_0000006
range: CARO_0000006
sub property of: BFO_0000051

synapsed_via_type_Ib_bouton_to
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002105
shorthand: synapsed_via_type_Ib_bouton_to
type: ObjectProperty
comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
sub property of: synapsed to
inverse of: synapsed_by_via_type_Ib_bouton

synapsed_via_type_Is_bouton_to
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002106
shorthand: synapsed_via_type_Is_bouton_to
type: ObjectProperty
comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
sub property of: synapsed to
inverse of: synapsed_by_via_type_Is_bouton

synapsed_via_type_II_bouton_to
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
has db xref: RO:0002107
shorthand: synapsed_via_type_II_bouton_to
type: ObjectProperty
comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
sub property of: synapsed to
inverse of: synapsed_by_via_type_II_bouton

synapsed_by_via_type_II_bouton
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002108
shorthand: synapsed_by_via_type_II_bouton
type: ObjectProperty
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
sub property of: synapsed by

synapsed_by_via_type_Ib_bouton
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002109
shorthand: synapsed_by_via_type_Ib_bouton
type: ObjectProperty
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
sub property of: synapsed by

has postsynaptic terminal in
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000118: synapsed in
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))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002110
shorthand: has_postsynaptic_terminal_in
type: ObjectProperty
domain: CL_0000540
sub property of: has synaptic terminal in
inverse of: has presynaptic terminal in

releases neurotransmitter
IAO_0000114: IAO_0000125
IAO_0000118: has neurotransmitter
has db xref: RO:0002111
shorthand: releases_neurotransmitter
type: ObjectProperty
domain: CARO_0000003
range: BFO_0000040
sub property of: topObjectProperty

synapsed_by_via_type_Is_bouton
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002112
shorthand: synapsed_by_via_type_Is_bouton
type: ObjectProperty
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
sub property of: synapsed by

has presynaptic terminal in
IAO_0000114: IAO_0000125
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
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?)
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002113
shorthand: has_presynaptic_terminal_in
type: ObjectProperty
domain: CL_0000540
sub property of: has synaptic terminal in

synapsed_via_type_III_bouton_to
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002114
shorthand: synapsed_via_type_III_bouton_to
type: ObjectProperty
comment: Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
sub property of: synapsed to
inverse of: synapsed_by_via_type_III_bouton

synapsed_by_via_type_III_bouton
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002115
shorthand: synapsed_by_via_type_III_bouton
type: ObjectProperty
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
sub property of: synapsed by

synapsed to
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
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?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002120
shorthand: 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))))
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
sub property of: sends output to

dendrite synapsed in
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
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)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002121
shorthand: dendrite_synapsed_in
type: ObjectProperty
domain: CL_0000540
sub property of: has postsynaptic terminal in

has synaptic terminal in
IAO_0000114: IAO_0000125
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_0000117: David Osumi-Sutherland
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?)
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002130
shorthand: has_synaptic_terminal_in
type: ObjectProperty
domain: CL_0000540
sub property of: overlaps

overlaps
IAO_0000114: IAO_0000125
IAO_0000115: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
has db xref: RO:0002131
in subset: ro-eco
in subset: valid for go annotation extension
in subset: valid for gocam
shorthand: overlaps
type: ObjectProperty
sub property of: mereotopologically related to

has fasciculating neuron projection
IAO_0000114: IAO_0000125
IAO_0000115: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: has fasciculating component
IAO_0000426: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002132
shorthand: has_fasciculating_neuron_projection
type: ObjectProperty
domain: CARO_0001001
range: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
sub property of: overlaps

innervates
IAO_0000114: IAO_0000125
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.
IAO_0000117: David Osumi-Sutherland
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?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
has db xref: RO:0002134
shorthand: innervates
type: ObjectProperty
domain: CARO_0001001
sub property of: topObjectProperty

continuous with
IAO_0000114: IAO_0000125
IAO_0000115: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: connected to
IAO_0000232: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO_0001900: RO_0001901
has db xref: RO:0002150
shorthand: continuous_with
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000004
sub property of: mereotopologically related to

partially overlaps
IAO_0000114: IAO_0000125
IAO_0000115: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
IAO_0000116: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
IAO_0000118: proper overlaps
IAO_0000426: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
RO_0001900: RO_0001901
has db xref: RO:0002151
in subset: ro-eco
shorthand: partially_overlaps
type: ObjectProperty
sub property of: overlaps

spatially disjoint from
IAO_0000114: IAO_0000125
IAO_0000115: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
has db xref: RO:0002163
in subset: ro-eco
shorthand: spatially_disjoint_from
type: ObjectProperty
sub property of: mereotopologically related to

connected to
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
has db xref: RO:0002170
shorthand: connected_to
type: ObjectProperty
domain: Restriction
  on property: BFO_0000050
  some values from: RO_0002577
range: Restriction
  on property: BFO_0000050
  some values from: RO_0002577
sub property of: mereotopologically related to

connects
IAO_0000112: The M8 connects Glasgow and Edinburgh
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
has db xref: RO:0002176
shorthand: connects
type: ObjectProperty
domain: BFO_0000004
range: Restriction
  on property: BFO_0000050
  some values from: RO_0002577
sub property of: mereotopologically related to

attached to part of
IAO_0000115: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
IAO_0000589: attached to part of (anatomical structure to anatomical structure)
has db xref: RO:0002177
shorthand: attached_to_part_of
type: ObjectProperty
domain: CARO_0000003
range: CARO_0000003
sub property of: mereotopologically related to
sub property of: biomechanically related to

supplies
IAO_0000115: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
has db xref: RO:0002178
shorthand: supplies
type: ObjectProperty
sub property of: connected to

drains
IAO_0000115: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
has db xref: RO:0002179
shorthand: drains
type: ObjectProperty
sub property of: connected to

has component
IAO_0000114: IAO_0000125
IAO_0000115: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
has db xref: RO:0002180
in subset: ro-eco
shorthand: has_component
type: ObjectProperty
sub property of: BFO_0000051

has phenotype
IAO_0000114: IAO_0000125
IAO_0000115: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
IAO_0000117: Chris Mungall
has db xref: RO:0002200
in subset: ro-eco
shorthand: has_phenotype
type: ObjectProperty
domain: Class
  union of: BFO_0000031
  union of: CARO_0000006
  union of: OGMS_0000031
range: UPHENO_0001001
sub property of: topObjectProperty
inverse of: phenotype of

phenotype of
IAO_0000114: IAO_0000125
IAO_0000115: inverse of has phenotype
IAO_0000117: Chris Mungall
has db xref: RO:0002201
in subset: RO_0002259
in subset: ro-eco
shorthand: phenotype_of
type: FunctionalProperty
type: ObjectProperty
sub property of: topObjectProperty

develops from
IAO_0000114: IAO_0000125
IAO_0000115: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Melissa Haendel
IAO_0000117: Terry Meehan
has db xref: RO:0002202
shorthand: develops_from
type: ObjectProperty
type: TransitiveProperty
comment: This is the transitive form of the develops from relation
domain: BFO_0000004
range: BFO_0000004
sub property of: developmentally preceded by
inverse of: develops into

develops into
IAO_0000114: IAO_0000125
IAO_0000115: inverse of develops from
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
has db xref: RO:0002203
in subset: RO_0002259
shorthand: develops_into
type: ObjectProperty
type: TransitiveProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into

directly develops from
IAO_0000114: IAO_0000125
IAO_0000115: Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: has developmental precursor
IAO_0000119: FBbt
RO_0002575: develops from
has db xref: RO:0002207
shorthand: directly_develops_from
type: ObjectProperty
comment: TODO - add child relations from DOS
domain: Class
  union of: CARO_0010000
  union of: CL_0000000
range: Class
  union of: CARO_0010000
  union of: CL_0000000
sub property of: develops from
inverse of: directly develops into

parasitoid of
IAO_0000115: A parasite that kills or sterilizes its host
has db xref: RO:0002208
shorthand: parasitoid_of
type: ObjectProperty
sub property of: parasite of
inverse of: has parasitoid

has parasitoid
IAO_0000115: inverse of parasitoid of
has db xref: RO:0002209
in subset: RO_0002259
shorthand: has_parasitoid
type: ObjectProperty
sub property of: parasitized by

directly develops into
IAO_0000114: IAO_0000125
IAO_0000115: inverse of directly develops from
IAO_0000118: developmental precursor of
has db xref: RO:0002210
in subset: RO_0002259
shorthand: directly_develops_into
type: ObjectProperty
sub property of: develops into

regulates
IAO_0000114: IAO_0000125
IAO_0000115: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
IAO_0000116: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
IAO_0000117: Chris Mungall
IAO_0000117: David Hill
IAO_0000117: Tanya Berardini
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
has db xref: RO:0002211
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: regulates
type: ObjectProperty
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
sub property of: causally upstream of
inverse of: regulated by

negatively regulates
IAO_0000115: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
has db xref: RO:0002212
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: negatively_regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by

positively regulates
IAO_0000115: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
has db xref: RO:0002213
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: positively_regulates
type: ObjectProperty
type: TransitiveProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by

capable of
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
IAO_0000115: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: Chris Mungall
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
has db xref: RO:0002215
in subset: ro-eco
shorthand: capable_of
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000015
sub property of: capable of part of

capable of part of
IAO_0000115: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: Chris Mungall
IAO_0000118: has function in
has db xref: RO:0002216
shorthand: capable_of_part_of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process

surrounded by
IAO_0000114: IAO_0000125
IAO_0000115: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
has db xref: RO:0002219
shorthand: surrounded_by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds

adjacent to
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: IAO_0000125
IAO_0000115: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
has db xref: RO:0002220
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: adjacent_to
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000004
sub property of: spatially disjoint from

surrounds
IAO_0000114: IAO_0000125
IAO_0000115: inverse of surrounded by
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
has db xref: RO:0002221
in subset: RO_0002259
shorthand: surrounds
type: ObjectProperty
sub property of: adjacent to

RO_0002222
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
has db xref: RO:0002222
in subset: ro-eco
shorthand: temporally_related_to
type: ObjectProperty

RO_0002223
IAO_0000117: Chris Mungall
has db xref: RO:0002223
in subset: ro-eco
shorthand: starts
type: ObjectProperty
sub property of: BFO_0000050

RO_0002224
IAO_0000117: Chris Mungall
has db xref: RO:0002224
in subset: ro-eco
shorthand: starts_with
type: ObjectProperty
sub property of: BFO_0000051

develops from part of
IAO_0000114: IAO_0000125
IAO_0000115: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
IAO_0000117: Chris Mungall
has db xref: RO:0002225
shorthand: develops_from_part_of
type: ObjectProperty
sub property of: develops from

develops in
IAO_0000114: IAO_0000125
IAO_0000115: x develops_in y if x is located in y whilst x is developing
IAO_0000117: Chris Mungall
IAO_0000119: EHDAA2
IAO_0000119: Jonathan Bard, EHDAA2
has db xref: RO:0002226
shorthand: develops_in
type: ObjectProperty
domain: CARO_0000000
sub property of: developmentally preceded by

obligate parasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.
has db xref: RO:0002227
shorthand: obligate_parasite_of
type: ObjectProperty
sub property of: parasite of

facultative parasite of
IAO_0000115: A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.
has db xref: RO:0002228
shorthand: facultative_parasite_of
type: ObjectProperty
sub property of: parasite of

RO_0002229
IAO_0000117: Chris Mungall
has db xref: RO:0002229
in subset: ro-eco
shorthand: ends
type: ObjectProperty
sub property of: BFO_0000050

RO_0002230
IAO_0000117: Chris Mungall
has db xref: RO:0002230
in subset: ro-eco
shorthand: ends_with
type: ObjectProperty
sub property of: BFO_0000051

has start location
IAO_0000114: IAO_0000125
IAO_0000115: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
IAO_0000117: Chris Mungall
IAO_0000118: starts with process that occurs in
has db xref: RO:0002231
in subset: ro-eco
shorthand: has_start_location
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000004
sub property of: has part that occurs in

has end location
IAO_0000114: IAO_0000125
IAO_0000115: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
IAO_0000117: Chris Mungall
IAO_0000118: ends with process that occurs in
has db xref: RO:0002232
in subset: ro-eco
shorthand: has_end_location
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000004
sub property of: has part that occurs in

has input
IAO_0000114: IAO_0000125
IAO_0000115: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: Chris Mungall
IAO_0000118: consumes
has db xref: RO:0002233
in subset: ro-eco
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_input
type: ObjectProperty
domain: BFO_0000015
sub property of: RO_0000057
inverse of: input of

has output
IAO_0000114: IAO_0000125
IAO_0000115: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
IAO_0000117: Chris Mungall
IAO_0000118: produces
has db xref: RO:0002234
in subset: ro-eco
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_output
type: ObjectProperty
sub property of: RO_0000057
inverse of: output of

stem parasite of
IAO_0000115: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)
has db xref: RO:0002235
shorthand: stem_parasite_of
type: ObjectProperty
sub property of: parasite of

root parasite of
IAO_0000115: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)
has db xref: RO:0002236
shorthand: root_parasite_of
type: ObjectProperty
sub property of: parasite of

hemiparasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.
has db xref: RO:0002237
shorthand: hemiparasite_of
type: ObjectProperty
sub property of: parasite of

has exposure receptor
IAO_0000115: A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
IAO_0000119: ExO:0000001
has db xref: RO:0002240
shorthand: has_exposure_receptor
type: ObjectProperty
sub property of: related via exposure to

has exposure stressor
IAO_0000115: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
IAO_0000119: ExO:0000000
has db xref: RO:0002241
shorthand: has_exposure_stressor
type: ObjectProperty
sub property of: has exposure stimulus

has exposure route
IAO_0000115: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
IAO_0000119: ExO:0000055
has db xref: RO:0002242
shorthand: has_exposure_route
type: ObjectProperty
sub property of: related via exposure to

has exposure transport path
IAO_0000115: A broad relationship between an exposure event or process and the course takes from the source to the target.
IAO_0000119: http://purl.obolibrary.org/obo/ExO_0000004
has db xref: RO:0002243
shorthand: has_exposure_transport_path
type: ObjectProperty
sub property of: related via exposure to

related via exposure to
IAO_0000115: Any relationship between an exposure event or process and any other entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.
has db xref: RO:0002244
shorthand: related_via_exposure_to
type: ObjectProperty
domain: RO_0002310
sub property of: causally related to

has active ingredient
IAO_0000112: Any portion of roundup 'has active ingredient' some glyphosate
IAO_0000115: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has db xref: RO:0002248
has exact synonym: has active substance
has related synonym: has active pharmaceutical ingredient
shorthand: has_active_ingredient
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: BFO_0000051
inverse of: active ingredient in

active ingredient in
IAO_0000115: inverse of has active ingredient
has db xref: RO:0002249
in subset: RO_0002259
shorthand: active_ingredient_in
type: ObjectProperty
sub property of: BFO_0000050

connecting branch of
IAO_0000115: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
has db xref: RO:0002252
shorthand: connecting_branch_of
type: ObjectProperty
sub property of: in branching relationship with
inverse of: has connecting branch

has connecting branch
IAO_0000115: inverse of connecting branch of
has db xref: RO:0002253
in subset: RO_0002259
shorthand: has_connecting_branch
type: ObjectProperty
sub property of: in branching relationship with

has developmental contribution from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: IAO_0000125
IAO_0000115: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: Chris Mungall
has db xref: RO:0002254
shorthand: has_developmental_contribution_from
type: ObjectProperty
domain: CARO_0000000
range: CARO_0000000
sub property of: developmentally preceded by
inverse of: developmentally contributes to

developmentally contributes to
IAO_0000114: IAO_0000125
IAO_0000115: inverse of has developmental contribution from
IAO_0000117: Chris Mungall
has db xref: RO:0002255
in subset: RO_0002259
shorthand: developmentally_contributes_to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to

developmentally induced by
IAO_0000114: IAO_0000125
IAO_0000115: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Melissa Haendel
IAO_0000118: induced by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
IAO_0000119: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
IAO_0000119: GO:0001759
IAO_0000232: We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
has db xref: RO:0002256
shorthand: developmentally_induced_by
type: ObjectProperty
domain: CARO_0000003
range: CARO_0000003
sub property of: developmentally preceded by
inverse of: developmentally induces

developmentally induces
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of developmentally induced by
IAO_0000117: Chris Mungall
has db xref: RO:0002257
shorthand: developmentally_induces
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally induce

developmentally preceded by
IAO_0000114: IAO_0000125
IAO_0000115: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
IAO_0000116: false
IAO_0000117: Chris Mungall
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
has db xref: RO:0002258
shorthand: developmentally_preceded_by
type: ObjectProperty
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
domain: BFO_0000002
range: BFO_0000002
sub property of: developmentally related to
inverse of: developmentally succeeded by

acts upstream of
IAO_0000112: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
IAO_0000115: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
has db xref: RO:0002263
in subset: valid for go gp2term
shorthand: acts_upstream_of
type: ObjectProperty
sub property of: acts upstream of or within

acts upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
IAO_0000115: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has db xref: RO:0002264
has related synonym: affects
in subset: valid for go gp2term
shorthand: acts_upstream_of_or_within
type: ObjectProperty
sub property of: causal agent in process

developmentally replaces
IAO_0000114: IAO_0000125
IAO_0000115: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
IAO_0000116: This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
IAO_0000117: Chris Mungall
IAO_0000118: replaces
has db xref: RO:0002285
shorthand: developmentally_replaces
type: ObjectProperty
sub property of: developmentally preceded by

developmentally succeeded by
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of developmentally preceded by
IAO_0000117: Chris Mungall
has db xref: RO:0002286
shorthand: developmentally_succeeded_by
type: ObjectProperty
sub property of: has developmental potential involving

part of developmental precursor of
IAO_0000112: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
has db xref: RO:0002287
shorthand: part_of_developmental_precursor_of
type: ObjectProperty
sub property of: developmentally succeeded by

results in developmental progression of
IAO_0000114: IAO_0000125
IAO_0000115: p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
IAO_0000116: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
IAO_0000117: Chris Mungall
has db xref: RO:0002295
shorthand: results_in_developmental_progression_of
type: ObjectProperty
domain: GO_0008150
range: CARO_0000003
sub property of: developmentally related to

results in development of
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000114: IAO_0000125
IAO_0000115: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
has db xref: RO:0002296
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_development_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

results in formation of
IAO_0000112: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
IAO_0000112: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
has db xref: RO:0002297
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_formation_of
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of

results in morphogenesis of
IAO_0000112: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
IAO_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: IAO_0000125
IAO_0000115: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
has db xref: RO:0002298
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_morphogenesis_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

results in maturation of
IAO_0000112: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
IAO_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: IAO_0000125
IAO_0000115: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
has db xref: RO:0002299
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_maturation_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

results in disappearance of
IAO_0000112: foramen ovale closure SubClassOf results in disappearance of foramen ovale
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000232: May be merged into parent relation
has db xref: RO:0002300
shorthand: results_in_disappearance_of
type: ObjectProperty
sub property of: results in ending of

results in developmental regression of
IAO_0000112: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000232: May be merged into parent relation
has db xref: RO:0002301
shorthand: results_in_developmental_regression_of
type: ObjectProperty
sub property of: results in ending of

is treated by substance
IAO_0000115: Inverse of 'is substance that treats'
creator: cjm
has db xref: RO:0002302
in subset: RO_0002259
shorthand: is_treated_by_substance
type: ObjectProperty
sub property of: causally related to
inverse of: is substance that treats

has habitat
IAO_0000112: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
IAO_0000114: IAO_0000428
IAO_0000115: x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
IAO_0000117: Pier Buttigieg
IAO_0000118: adapted for living in
has db xref: RO:0002303
in subset: ro-eco
shorthand: has_habitat
type: ObjectProperty
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
domain: CARO_0001010
range: ENVO_01000254
sub property of: ecologically related to

causally upstream of, positive effect
RO_0004049: causally upstream of
creator: cjm
has db xref: RO:0002304
in subset: valid for go annotation extension
in subset: valid for gocam
shorthand: causally_upstream_of,_positive_effect
type: ObjectProperty
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect

causally upstream of, negative effect
RO_0004050: causally upstream of
creator: cjm
has db xref: RO:0002305
shorthand: causally_upstream_of,_negative_effect
type: ObjectProperty
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect

has exposure stimulus
IAO_0000115: A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
contributor: Austin Meier
contributor: Chris Mungall
contributor: Marie Angelique Laporte
created by: cjm
creation date: 2017-06-05T17:35:04Z
has db xref: RO:0002309
shorthand: has_exposure_stimulus
type: ObjectProperty
sub property of: related via exposure to

transports or maintains localization of
IAO_0000115: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
IAO_0000117: Chris Mungall
IAO_0000118: regulates localization of
has db xref: RO:0002313
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: transports_or_maintains_localization_of
type: ObjectProperty
sub property of: related via localization to
sub property of: has anatomical participant

results in acquisition of features of
IAO_0000112: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
IAO_0000115: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
has db xref: RO:0002315
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_acquisition_of_features_of
type: ObjectProperty
range: CARO_0000003
sub property of: results in developmental progression of
sub property of: has anatomical participant

ecologically related to
IAO_0000115: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
has db xref: RO:0002321
in subset: ro-eco
shorthand: ecologically_related_to
type: ObjectProperty

confers advantage in
IAO_0000116: An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
IAO_0000117: Chris Mungall
IAO_0000118: adapted for
has db xref: RO:0002322
in subset: ro-eco
shorthand: confers_advantage_in
type: ObjectProperty
range: ENVO_01000254
sub property of: ecologically related to

mereotopologically related to
IAO_0000115: A mereological relationship or a topological relationship
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901
has db xref: RO:0002323
shorthand: mereotopologically_related_to
type: ObjectProperty

developmentally related to
IAO_0000115: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
has db xref: RO:0002324
shorthand: developmentally_related_to
type: ObjectProperty

colocalizes with
IAO_0000112: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
IAO_0000115: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
creator: Gene Ontology Consortium
has db xref: RO:0002325
in subset: valid for go gp2term
shorthand: colocalizes_with
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: mereotopologically related to

contributes to
IAO_0000112: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
IAO_0000112: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
IAO_0000112: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
IAO_0000116: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
has db xref: RO:0002326
in subset: valid for go gp2term
shorthand: contributes_to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of

enables
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
IAO_0000117: Chris Mungall
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
IAO_0000232: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
has db xref: RO:0002327
in subset: valid for go gp2term
shorthand: enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by

functionally related to
IAO_0000115: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function
has db xref: RO:0002328
shorthand: functionally_related_to
type: ObjectProperty

part of structure that is capable of
IAO_0000115: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: Chris Mungall
IAO_0000118: false
has db xref: RO:0002329
shorthand: part_of_structure_that_is_capable_of
type: ObjectProperty
sub property of: functionally related to

involved in
IAO_0000115: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: Chris Mungall
IAO_0000118: actively involved in
IAO_0000118: enables part of
has db xref: RO:0002331
shorthand: involved_in
type: ObjectProperty
sub property of: RO_0000056
sub property of: involved in or involved in regulation of

regulates levels of
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
IAO_0000115: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: regulates levels of (process to entity)
has db xref: RO:0002332
shorthand: regulates_levels_of
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000040
sub property of: functionally related to

enabled by
IAO_0000115: inverse of enables
IAO_0000117: Chris Mungall
has db xref: RO:0002333
in subset: valid for gocam
shorthand: enabled_by
type: ObjectProperty
sub property of: RO_0000057
sub property of: functionally related to

regulated by
IAO_0000115: inverse of regulates
IAO_0000117: Chris Mungall
IAO_0000589: regulated by (processual)
has db xref: RO:0002334
in subset: RO_0002259
shorthand: regulated_by
type: ObjectProperty
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
sub property of: causally downstream of or within

negatively regulated by
IAO_0000115: inverse of negatively regulates
IAO_0000117: Chris Mungall
has db xref: RO:0002335
in subset: RO_0002259
shorthand: negatively_regulated_by
type: ObjectProperty
sub property of: regulated by

positively regulated by
IAO_0000115: inverse of positively regulates
IAO_0000117: Chris Mungall
has db xref: RO:0002336
in subset: RO_0002259
shorthand: positively_regulated_by
type: ObjectProperty
sub property of: regulated by

related via localization to
IAO_0000115: A relationship that holds via some process of localization
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is a grouping relation.
has db xref: RO:0002337
shorthand: related_via_localization_to
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000002

has target start location
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
IAO_0000117: Chris Mungall
has db xref: RO:0002338
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_target_start_location
type: ObjectProperty
sub property of: results in transport to from or in

has target end location
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
IAO_0000117: Chris Mungall
has db xref: RO:0002339
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_target_end_location
type: ObjectProperty
sub property of: results in transport to from or in

imports
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
IAO_0000117: Chris Mungall
has db xref: RO:0002340
in subset: valid for go ontology
shorthand: imports
type: ObjectProperty
sub property of: transports

results in transport along
IAO_0000115: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
IAO_0000117: Chris Mungall
has db xref: RO:0002341
shorthand: results_in_transport_along
type: ObjectProperty
sub property of: related via localization to

results in transport across
IAO_0000115: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
IAO_0000117: Chris Mungall
has db xref: RO:0002342
in subset: valid for go ontology
shorthand: results_in_transport_across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in

results in growth of
IAO_0000112: 'pollen tube growth' results_in growth_of some 'pollen tube'
IAO_0000117: Chris Mungall
has db xref: RO:0002343
shorthand: results_in_growth_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

results in transport to from or in
IAO_0000112: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
IAO_0000117: Chris Mungall
has db xref: RO:0002344
shorthand: results_in_transport_to_from_or_in
type: ObjectProperty
sub property of: related via localization to

exports
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
IAO_0000117: Chris Mungall
has db xref: RO:0002345
in subset: valid for go ontology
shorthand: exports
type: ObjectProperty
sub property of: transports

results in commitment to
IAO_0000112: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
IAO_0000115: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate
has db xref: RO:0002348
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_commitment_to
type: ObjectProperty
range: CL_0000000
sub property of: results in developmental progression of

results in determination of
IAO_0000115: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate
has db xref: RO:0002349
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_determination_of
type: ObjectProperty
range: CL_0000000
sub property of: results in developmental progression of

input of
IAO_0000115: inverse of has input
IAO_0000117: Chris Mungall
has db xref: RO:0002352
in subset: RO_0002259
in subset: ro-eco
shorthand: input_of
type: ObjectProperty
sub property of: RO_0000056
sub property of: functionally related to

output of
IAO_0000115: inverse of has output
IAO_0000117: Chris Mungall
has db xref: RO:0002353
in subset: RO_0002259
in subset: ro-eco
shorthand: output_of
type: ObjectProperty
sub property of: RO_0000056
sub property of: functionally related to

formed as result of
IAO_0000117: Chris Mungall
has db xref: RO:0002354
shorthand: formed_as_result_of
type: ObjectProperty
sub property of: output of

results in structural organization of
IAO_0000115: A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
IAO_0000117: Chris Mungall
has db xref: RO:0002355
shorthand: results_in_structural_organization_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

results in specification of
IAO_0000115: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate
has db xref: RO:0002356
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_specification_of
type: ObjectProperty
range: CL_0000000
sub property of: results in developmental progression of

results in developmental induction of
IAO_0000115: p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
IAO_0000117: Chris Mungall
has db xref: RO:0002357
shorthand: results_in_developmental_induction_of
type: ObjectProperty
sub property of: results in developmental progression of

has dendrite location
IAO_0000117: Chris Mungall
source: http://neurolex.org/wiki/Property:DendriteLocation
has db xref: RO:0002360
shorthand: has_dendrite_location
type: ObjectProperty
sub property of: overlaps

attached to
IAO_0000115: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
IAO_0000117: Chris Mungall
IAO_0000589: attached to (anatomical structure to anatomical structure)
has db xref: RO:0002371
in subset: ro-eco
shorthand: attached_to
type: ObjectProperty
type: SymmetricProperty
sub property of: connected to
sub property of: attached to part of

has muscle origin
IAO_0000115: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Insertion_(anatomy)
has db xref: RO:0002372
shorthand: has_muscle_origin
type: ObjectProperty
domain: CARO_0000003
sub property of: attached to
sub property of: biomechanically related to

has muscle insertion
IAO_0000115: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Insertion_(anatomy)
has db xref: RO:0002373
shorthand: has_muscle_insertion
type: ObjectProperty
domain: CARO_0000003
sub property of: attached to
sub property of: biomechanically related to

in branching relationship with
IAO_0000114: IAO_0000428
IAO_0000115: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
has db xref: RO:0002375
shorthand: in_branching_relationship_with
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: BFO_0000050
sub property of: mereotopologically related to

tributary of
IAO_0000112: Deschutes River tributary_of Columbia River
IAO_0000112: inferior epigastric vein tributary_of external iliac vein
IAO_0000114: IAO_0000428
IAO_0000115: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
IAO_0000117: Chris Mungall
IAO_0000118: drains into
IAO_0000118: drains to
IAO_0000118: tributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Tributary
IAO_0000119: http://www.medindia.net/glossary/venous_tributary.htm
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
has db xref: RO:0002376
in subset: ro-eco
shorthand: tributary_of
type: ObjectProperty
sub property of: in branching relationship with

distributary of
IAO_0000112: Deschutes River distributary_of Little Lava Lake
IAO_0000114: IAO_0000428
IAO_0000115: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
IAO_0000117: Chris Mungall
IAO_0000118: branch of
IAO_0000118: distributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Distributary
has db xref: RO:0002377
in subset: ro-eco
shorthand: distributary_of
type: ObjectProperty
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes
sub property of: in branching relationship with

anabranch of
IAO_0000114: IAO_0000428
IAO_0000115: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
IAO_0000117: Chris Mungall
IAO_0000118: anastomoses with
has db xref: RO:0002378
in subset: ro-eco
shorthand: anabranch_of
type: ObjectProperty
sub property of: distributary of
sub property of:
  inverse of: tributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of

spatially coextensive with
IAO_0000112: A lump of clay and a statue
IAO_0000115: x spatially_coextensive_with y if and inly if x and y have the same location
IAO_0000117: Chris Mungall
IAO_0000232: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
has db xref: RO:0002379
shorthand: spatially_coextensive_with
type: ObjectProperty
sub property of: overlaps

branching part of
IAO_0000114: IAO_0000428
IAO_0000115: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
IAO_0000117: Chris Mungall
has db xref: RO:0002380
in subset: ro-eco
shorthand: branching_part_of
type: ObjectProperty
range: Restriction
  on property: RO_0000053
  some values from: PATO_0000402
sub property of: BFO_0000050
sub property of: in branching relationship with
inverse of: has branching part

main stem of
IAO_0000114: IAO_0000428
IAO_0000115: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
IAO_0000117: Chris Mungall
has db xref: RO:0002381
in subset: ro-eco
shorthand: main_stem_of
type: ObjectProperty
sub property of: in branching relationship with

proper distributary of
IAO_0000114: IAO_0000428
IAO_0000115: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
IAO_0000117: Chris Mungall
has db xref: RO:0002382
in subset: ro-eco
shorthand: proper_distributary_of
type: ObjectProperty
sub property of: distributary of

proper tributary of
IAO_0000114: IAO_0000428
IAO_0000115: x proper_tributary_of y iff x tributary_of y and x does not originate from y
IAO_0000117: Chris Mungall
has db xref: RO:0002383
in subset: ro-eco
shorthand: proper_tributary_of
type: ObjectProperty
sub property of: tributary of

has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000117: Chris Mungall
has db xref: RO:0002384
shorthand: has_developmental_potential_involving
type: ObjectProperty
domain: CARO_0000000
range: CARO_0000000
sub property of: developmentally related to

has potential to developmentally contribute to
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: Chris Mungall
has db xref: RO:0002385
shorthand: has_potential_to_developmentally_contribute_to
type: ObjectProperty
sub property of: has developmental potential involving

has potential to developmentally induce
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
IAO_0000117: Chris Mungall
has db xref: RO:0002386
shorthand: has_potential_to_developmentally_induce
type: ObjectProperty
sub property of: has developmental potential involving

has potential to develop into
IAO_0000114: IAO_0000428
IAO_0000115: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: Chris Mungall
has db xref: RO:0002387
shorthand: has_potential_to_develop_into
type: ObjectProperty
sub property of: has developmental potential involving

has potential to directly develop into
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: Chris Mungall
has db xref: RO:0002388
shorthand: has_potential_to_directly_develop_into
type: ObjectProperty
sub property of: has potential to develop into

has direct input
IAO_0000112: 'protein catabolic process' SubClassOf has_direct_input some protein
IAO_0000114: IAO_0000428
IAO_0000115: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: Chris Mungall
IAO_0000118: directly consumes
IAO_0000232: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has db xref: RO:0002400
shorthand: has_direct_input
type: ObjectProperty
sub property of: has input

causally downstream of
IAO_0000114: IAO_0000428
IAO_0000115: inverse of upstream of
IAO_0000117: Chris Mungall
has db xref: RO:0002404
shorthand: causally_downstream_of
type: ObjectProperty
sub property of: BFO_0000062
sub property of: causally downstream of or within
inverse of: causally upstream of

immediately causally downstream of
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall
has db xref: RO:0002405
shorthand: immediately_causally_downstream_of
type: ObjectProperty
sub property of: RO_0002087
sub property of: causally downstream of
inverse of: immediately causally upstream of

directly activates
IAO_0000114: IAO_0000428
IAO_0000115: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
IAO_0000117: Chris Mungall
IAO_0000118: directly positively regulates
IAO_0000119: causal-relations
IAO_0000589: directly activates (process to process)
has db xref: RO:0002406
shorthand: directly_activates
type: ObjectProperty
sub property of: directly positively regulates

indirectly activates
IAO_0000115: p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.
IAO_0000117: Chris Mungall
IAO_0000118: indirectly positively regulates
RO_0002579: positively regulates
has db xref: RO:0002407
shorthand: indirectly_activates
type: ObjectProperty
type: TransitiveProperty
sub property of: positively regulates

directly inhibits
IAO_0000117: Chris Mungall
IAO_0000118: directly negatively regulates
IAO_0000119: causal-relations
IAO_0000589: directly inhibits (process to process)
has db xref: RO:0002408
shorthand: directly_inhibits
type: ObjectProperty
sub property of: directly negatively regulates

indirectly inhibits
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall
IAO_0000118: indirectly negatively regulates
RO_0002579: negatively regulates
has db xref: RO:0002409
shorthand: indirectly_inhibits
type: ObjectProperty
type: TransitiveProperty
sub property of: negatively regulates

causally related to
IAO_0000114: IAO_0000428
IAO_0000115: This relation groups causal relations between material entities and causal relations between processes
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
has db xref: RO:0002410
shorthand: causally_related_to
type: ObjectProperty

causally upstream of
IAO_0000114: IAO_0000428
IAO_0000115: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
IAO_0000117: Chris Mungall
has db xref: RO:0002411
in subset: valid for go annotation extension
in subset: valid for gocam
shorthand: causally_upstream_of
type: ObjectProperty
type: TransitiveProperty
sub property of: BFO_0000063
sub property of: causally upstream of or within

immediately causally upstream of
IAO_0000114: IAO_0000428
IAO_0000115: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
IAO_0000117: Chris Mungall
RO_0002575: causally upstream of
has db xref: RO:0002412
shorthand: immediately_causally_upstream_of
type: ObjectProperty
sub property of: RO_0002090
sub property of: causally upstream of

directly provides input for
IAO_0000114: IAO_0000428
IAO_0000115: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
IAO_0000116: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly provides input for (process to process)
has db xref: RO:0002413
shorthand: directly_provides_input_for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for

transitively provides input for
IAO_0000114: IAO_0000428
IAO_0000115: transitive form of directly_provides_input_for
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
IAO_0000589: transitively provides input for (process to process)
has db xref: RO:0002414
shorthand: transitively_provides_input_for
type: ObjectProperty
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
sub property of: causally upstream of

causally upstream of or within
IAO_0000115: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: Chris Mungall
IAO_0000118: influences (processual)
has db xref: RO:0002418
has related synonym: affects
shorthand: causally_upstream_of_or_within
type: ObjectProperty
type: TransitiveProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within

causally downstream of or within
IAO_0000115: inverse of causally upstream of or within
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
has db xref: RO:0002427
in subset: RO_0002259
shorthand: causally_downstream_of_or_within
type: ObjectProperty
type: TransitiveProperty
sub property of: causal relation between processes

involved in regulation of
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: Chris Mungall
has db xref: RO:0002428
shorthand: involved_in_regulation_of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of

involved in positive regulation of
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: Chris Mungall
RO_0004049: involved in regulation of
has db xref: RO:0002429
shorthand: involved_in_positive_regulation_of
type: ObjectProperty
sub property of: involved in regulation of

involved in negative regulation of
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: Chris Mungall
RO_0004050: involved in regulation of
has db xref: RO:0002430
shorthand: involved_in_negative_regulation_of
type: ObjectProperty
sub property of: involved in regulation of

involved in or involved in regulation of
IAO_0000115: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: Chris Mungall
IAO_0000118: involved in or reguates
has db xref: RO:0002431
shorthand: involved_in_or_involved_in_regulation_of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process

is active in
IAO_0000112: A protein that enables activity in a cytosol.
IAO_0000115: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
IAO_0000117: Chris Mungall
IAO_0000118: executes activity in
has db xref: RO:0002432
has exact synonym: enables activity in
shorthand: is_active_in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to

contributes to morphology of
IAO_0000115: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
IAO_0000117: Chris Mungall
has db xref: RO:0002433
shorthand: contributes_to_morphology_of
type: ObjectProperty
sub property of: overlaps

interacts with
IAO_0000115: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_0000117: Chris Mungall
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has db xref: RO:0002434
has exact synonym: in pairwise interaction with
in subset: ro-eco
shorthand: interacts_with
type: ObjectProperty
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040

genetically interacts with
IAO_0000116: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
IAO_0000117: Chris Mungall
has db xref: RO:0002435
shorthand: genetically_interacts_with
type: ObjectProperty
type: SymmetricProperty
sub property of: interacts with

molecularly interacts with
IAO_0000115: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: Chris Mungall
IAO_0000118: binds
IAO_0000118: molecularly binds with
has db xref: RO:0002436
shorthand: molecularly_interacts_with
type: ObjectProperty
type: SymmetricProperty
sub property of: interacts with

biotically interacts with
IAO_0000115: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000117: Chris Mungall
IAO_0000118: interacts with on organism level
has db xref: RO:0002437
in subset: ro-eco
shorthand: biotically_interacts_with
type: ObjectProperty
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: ecologically related to
sub property of: interacts with

trophically interacts with
IAO_0000115: An interaction relationship in which the partners are related via a feeding relationship.
IAO_0000117: Chris Mungall
has db xref: RO:0002438
in subset: ro-eco
shorthand: trophically_interacts_with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

preys on
IAO_0000112: A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
IAO_0000112: Baleen whale preys on krill
IAO_0000115: An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
IAO_0000117: Chris Mungall
IAO_0000117: Jorrit Poelen
IAO_0000117: Katja Shulz
IAO_0000118: is subject of predation interaction with
IAO_0000118: preys upon
has db xref: RO:0002439
in subset: ro-eco
shorthand: preys_on
type: ObjectProperty
sub property of: trophically interacts with
inverse of: preyed upon by

symbiotically interacts with
IAO_0000115: A biotic interaction in which the two organisms live together in more or less intimate association.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
RO_0002561: GO_0044403
has db xref: RO:0002440
in subset: ro-eco
shorthand: symbiotically_interacts_with
type: ObjectProperty
type: SymmetricProperty
sub property of: participates in a biotic-biotic interaction with

commensually interacts with
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
RO_0002561: GO_0085031
has db xref: RO:0002441
in subset: ro-eco
shorthand: commensually_interacts_with
type: ObjectProperty
sub property of: symbiotically interacts with

mutualistically interacts with
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
RO_0002561: GO_0085030
has db xref: RO:0002442
in subset: ro-eco
shorthand: mutualistically_interacts_with
type: ObjectProperty
sub property of: symbiotically interacts with

interacts with via parasite-host interaction
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: This relation groups a pair of inverse relations, parasite of and parasitized by
RO_0002561: GO_0072519
has db xref: RO:0002443
in subset: ro-eco
shorthand: interacts_with_via_parasite-host_interaction
type: ObjectProperty
sub property of: symbiotically interacts with

parasite of
IAO_0000112: Pediculus humanus capitis parasite of human
IAO_0000117: Chris Mungall
IAO_0000118: parasitizes
RO_0002560: GO_0072519
has db xref: RO:0002444
has exact synonym: direct parasite of
in subset: ro-eco
shorthand: parasite_of
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: has host
inverse of: parasitized by

parasitized by
IAO_0000117: Chris Mungall
IAO_0000118: has parasite
IAO_0000118: parasitised by
has db xref: RO:0002445
has exact synonym: directly parasitized by
in subset: ro-eco
shorthand: parasitized_by
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: host of

participates in a abiotic-biotic interaction with
IAO_0000112: Porifiera attaches to substrate
IAO_0000115: A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
IAO_0000117: Chris Mungall
has db xref: RO:0002446
has related synonym: semibiotically interacts with
in subset: ro-eco
shorthand: participates_in_a_abiotic-biotic_interaction_with
type: ObjectProperty
sub property of: biotically interacts with

phosphorylates
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
has db xref: RO:0002447
shorthand: phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with

directly regulates activity of
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
has db xref: RO:0002448
has exact synonym: molecularly controls
shorthand: directly_regulates_activity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: molecularly interacts with
sub property of: regulates activity of

directly negatively regulates activity of
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly inhibits
has db xref: RO:0002449
has exact synonym: molecularly decreases activity of
shorthand: directly_negatively_regulates_activity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly regulates activity of

directly positively regulates activity of
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly activates
has db xref: RO:0002450
has exact synonym: molecularly increases activity of
shorthand: directly_positively_regulates_activity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly regulates activity of

transmitted by
IAO_0000112: all dengue disease transmitted by some mosquito
IAO_0000115: A relationship that holds between a disease and organism
IAO_0000116: Add domain and range constraints
IAO_0000117: Chris Mungall
has db xref: RO:0002451
shorthand: transmitted_by
type: ObjectProperty
sub property of: ecologically related to

has symptom
IAO_0000115: A relation that holds between a disease or an organism and a phenotype
IAO_0000117: Chris Mungall
has db xref: RO:0002452
shorthand: has_symptom
type: ObjectProperty
domain: OGMS_0000031
sub property of: has phenotype

host of
IAO_0000117: Chris Mungall
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
has db xref: RO:0002453
in subset: ro-eco
shorthand: host_of
type: ObjectProperty
sub property of: symbiotically interacts with

has host
IAO_0000115: X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
IAO_0000117: Chris Mungall
has db xref: RO:0002454
in subset: ro-eco
shorthand: has_host
type: ObjectProperty
sub property of: symbiotically interacts with

pollinates
IAO_0000112: Bees pollinate Flowers
IAO_0000116: This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
IAO_0000117: Chris Mungall
IAO_0000118: is subject of pollination interaction with
has db xref: RO:0002455
in subset: ro-eco
shorthand: pollinates
type: ObjectProperty
sub property of: mutualistically interacts with
inverse of: pollinated by

pollinated by
IAO_0000117: Chris Mungall
IAO_0000118: has polinator
IAO_0000118: is target of pollination interaction with
has db xref: RO:0002456
in subset: ro-eco
shorthand: pollinated_by
type: ObjectProperty
sub property of: mutualistically interacts with

acquires nutrients from
IAO_0000117: Chris Mungall
IAO_0000232: Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
has db xref: RO:0002457
in subset: ro-eco
shorthand: acquires_nutrients_from
type: ObjectProperty
sub property of: trophically interacts with
inverse of: provides nutrients for

preyed upon by
IAO_0000115: inverse of preys on
IAO_0000117: Chris Mungall
IAO_0000118: has predator
IAO_0000118: is target of predation interaction with
has db xref: RO:0002458
in subset: RO_0002259
in subset: ro-eco
shorthand: preyed_upon_by
type: ObjectProperty
sub property of: trophically interacts with

is vector for
IAO_0000112: Anopheles is a vector for Plasmodium
IAO_0000117: Chris Mungall
IAO_0000119: a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
has db xref: RO:0002459
in subset: ro-eco
shorthand: is_vector_for
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: has vector

has vector
IAO_0000117: Chris Mungall
has db xref: RO:0002460
in subset: ro-eco
shorthand: has_vector
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

partner in
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
has db xref: RO:0002461
shorthand: partner_in
type: ObjectProperty
sub property of: RO_0000056

subject participant in
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
has db xref: RO:0002462
shorthand: subject_participant_in
type: ObjectProperty
sub property of: partner in

target participant in
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
has db xref: RO:0002463
shorthand: target_participant_in
type: ObjectProperty
sub property of: partner in

provides nutrients for
IAO_0000117: Chris Mungall
has db xref: RO:0002469
in subset: ro-eco
shorthand: provides_nutrients_for
type: ObjectProperty
sub property of: trophically interacts with

eats
IAO_0000117: Chris Mungall
IAO_0000118: is subject of eating interaction with
has db xref: RO:0002470
in subset: ro-eco
shorthand: eats
type: ObjectProperty
sub property of: trophically interacts with

is eaten by
IAO_0000117: Chris Mungall
IAO_0000118: eaten by
IAO_0000118: is target of eating interaction with
has db xref: RO:0002471
in subset: ro-eco
shorthand: is_eaten_by
type: ObjectProperty
sub property of: trophically interacts with

composed primarily of
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
IAO_0000115: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
RO_0001900: RO_0001901
has db xref: RO:0002473
in subset: ro-eco
shorthand: composed_primarily_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: BFO_0000051

child nucleus of
IAO_0000112: ABal nucleus child nucleus of ABa nucleus (in C elegans)
IAO_0000115: c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
IAO_0000117: Chris Mungall
IAO_0000232: This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.
has db xref: RO:0002476
shorthand: child_nucleus_of
type: ObjectProperty
domain: GO_0005634
range: GO_0005634
sub property of: developmentally preceded by

child nucleus of in hermaphrodite
IAO_0000115: A child nucleus relationship in which the cells are part of a hermaphroditic organism
IAO_0000117: Chris Mungall
has db xref: RO:0002477
shorthand: child_nucleus_of_in_hermaphrodite
type: ObjectProperty
sub property of: child nucleus of

child nucleus of in male
IAO_0000115: A child nucleus relationship in which the cells are part of a male organism
IAO_0000117: Chris Mungall
has db xref: RO:0002478
shorthand: child_nucleus_of_in_male
type: ObjectProperty
sub property of: child nucleus of

has part that occurs in
IAO_0000115: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
IAO_0000117: Chris Mungall
has db xref: RO:0002479
in subset: ro-eco
shorthand: has_part_that_occurs_in
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000004

ubiquitinates
IAO_0000115: An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
has db xref: RO:0002480
shorthand: ubiquitinates
type: ObjectProperty
sub property of: molecularly interacts with

receives input from
IAO_0000116: See notes for inverse relation
IAO_0000117: Chris Mungall
has db xref: RO:0002485
shorthand: receives_input_from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to

sends output to
IAO_0000116: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
IAO_0000117: Chris Mungall
has db xref: RO:0002486
shorthand: sends_output_to
type: ObjectProperty
sub property of: connected to

transformation of
IAO_0000115: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
IAO_0000117: Chris Mungall
has db xref: RO:0002494
shorthand: transformation_of
type: ObjectProperty
type: TransitiveProperty
sub property of: develops from

immediate transformation of
IAO_0000115: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
IAO_0000117: Chris Mungall
RO_0002575: transformation of
has db xref: RO:0002495
shorthand: immediate_transformation_of
type: ObjectProperty
sub property of: directly develops from
sub property of: transformation of

causal agent in process
IAO_0000115: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations
has db xref: RO:0002500
shorthand: causal_agent_in_process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent

causal relation between processes
IAO_0000115: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
has db xref: RO:0002501
shorthand: causal_relation_between_processes
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000003
sub property of: causally related to

has intermediate
IAO_0000112: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
IAO_0000115: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
IAO_0000117: Chris Mungall
IAO_0000118: has intermediate product
has db xref: RO:0002505
in subset: ro-eco
shorthand: has_intermediate
type: ObjectProperty
sub property of: RO_0000057

causal relation between entities
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
has db xref: RO:0002506
shorthand: causal_relation_between_entities
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000002
sub property of: causally related to

determined by
IAO_0000112: A coral reef environment is determined by a particular coral reef
IAO_0000115: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
IAO_0000116: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/24330602
IAO_0000589: determined by (system to material entity)
creator: Chris Mungall
creator: Pier Buttigieg
has db xref: RO:0002507
in subset: ro-eco
shorthand: determined_by
type: ObjectProperty
domain: RO_0002577
range: BFO_0000040
sub property of: BFO_0000050
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines

determines
IAO_0000115: inverse of determined by
IAO_0000117: Chris Mungall
IAO_0000589: determines (material entity to system)
has db xref: RO:0002508
in subset: RO_0002259
in subset: ro-eco
shorthand: determines
type: ObjectProperty
sub property of: causally influences

determined by part of
IAO_0000115: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
IAO_0000117: Chris Mungall
has db xref: RO:0002509
in subset: ro-eco
shorthand: determined_by_part_of
type: ObjectProperty
domain: RO_0002577
range: BFO_0000040
sub property of: overlaps
sub property of: causal relation between entities

sequentially related to
IAO_0000115: A relation that holds between two entities that have the property of being sequences or having sequences.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000232: The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
cites as authority: 006650.abstract
has db xref: RO:0002514
shorthand: sequentially_related_to
type: ObjectProperty
domain: RO_0002532
range: RO_0002532

sequentially adjacent to
IAO_0000112: Every UTR is adjacent to a CDS of the same transcript
IAO_0000112: Two consecutive DNA residues are sequentially adjacent
IAO_0000112: Two exons on a processed transcript that were previously connected by an intron are adjacent
IAO_0000115: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002515
shorthand: sequentially_adjacent_to
type: ObjectProperty
sub property of: does not overlap sequence of

has start sequence
IAO_0000112: Every CDS has as a start sequence the start codon for that transcript
IAO_0000115: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
IAO_0000117: Chris Mungall
IAO_0000118: started by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002516
shorthand: has_start_sequence
type: ObjectProperty
type: TransitiveProperty
sub property of: has subsequence
inverse of: is start sequence of

is start sequence of
IAO_0000115: inverse of has start sequence
IAO_0000117: Chris Mungall
IAO_0000118: starts
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002517
in subset: RO_0002259
shorthand: is_start_sequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: is subsequence of

has end sequence
IAO_0000112: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
IAO_0000115: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
IAO_0000117: Chris Mungall
IAO_0000118: ended by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002518
shorthand: has_end_sequence
type: ObjectProperty
type: TransitiveProperty
sub property of: has subsequence
inverse of: is end sequence of

is end sequence of
IAO_0000115: inverse of has end sequence
IAO_0000117: Chris Mungall
IAO_0000118: ends
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002519
in subset: RO_0002259
shorthand: is_end_sequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: is subsequence of

is consecutive sequence of
IAO_0000115: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
IAO_0000116: In the SO paper, this was defined as an instance-type relation
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002520
shorthand: is_consecutive_sequence_of
type: ObjectProperty
sub property of: has subsequence

is sequentially aligned with
IAO_0000112: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
IAO_0000115: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002521
shorthand: is_sequentially_aligned_with
type: ObjectProperty
type: SymmetricProperty
sub property of: sequentially related to

bounds sequence of
IAO_0000112: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
IAO_0000115: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002522
shorthand: bounds_sequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: sequentially related to
inverse of: is bound by sequence of

is bound by sequence of
IAO_0000115: inverse of bounds sequence of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002523
in subset: RO_0002259
shorthand: is_bound_by_sequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: sequentially related to

has subsequence
IAO_0000115: x has subsequence y iff all of the sequence parts of x are sequence parts of y
IAO_0000117: Chris Mungall
IAO_0000118: contains
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
has db xref: RO:0002524
shorthand: has_subsequence
type: ObjectProperty
type: TransitiveProperty
sub property of: BFO_0000051
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of

is subsequence of
IAO_0000115: inverse of has subsequence
IAO_0000117: Chris Mungall
IAO_0000118: contained by
cites as authority: 006650.abstract
has db xref: RO:0002525
in subset: RO_0002259
shorthand: is_subsequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: BFO_0000050
sub property of: is bound by sequence of
sub property of: overlaps sequence of

overlaps sequence of
IAO_0000115: x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002526
shorthand: overlaps_sequence_of
type: ObjectProperty
type: SymmetricProperty
sub property of: overlaps
sub property of: sequentially related to

does not overlap sequence of
IAO_0000115: x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
IAO_0000117: Chris Mungall
IAO_0000118: disconnected from
cites as authority: 006650.abstract
has db xref: RO:0002527
shorthand: does_not_overlap_sequence_of
type: ObjectProperty
type: SymmetricProperty
sub property of: sequentially related to

is upstream of sequence of
IAO_0000115: inverse of downstream of sequence of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002528
shorthand: is_upstream_of_sequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: does not overlap sequence of

is downstream of sequence of
IAO_0000115: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002529
shorthand: is_downstream_of_sequence_of
type: ObjectProperty
type: TransitiveProperty
sub property of: does not overlap sequence of

is immediately downstream of sequence of
IAO_0000112: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
IAO_0000117: Chris Mungall
RO_0002575: is downstream of sequence of
cites as authority: 006650.abstract
has db xref: RO:0002530
shorthand: is_immediately_downstream_of_sequence_of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of

is immediately upstream of sequence of
IAO_0000112: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: inverse of immediately downstream of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
has db xref: RO:0002531
shorthand: is_immediately_upstream_of_sequence_of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of

has skeleton
IAO_0000112: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
IAO_0000115: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
IAO_0000117: Chris Mungall
IAO_0000118: has supporting framework
IAO_0000232: The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
has db xref: RO:0002551
shorthand: has_skeleton
type: AsymmetricProperty
type: IrreflexiveProperty
type: ObjectProperty
domain: CARO_0000003
range: CARO_0000006
sub property of: BFO_0000051
inverse of: skeleton of

results in ending of
IAO_0000115: p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
IAO_0000117: Chris Mungall
has db xref: RO:0002552
shorthand: results_in_ending_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

hyperparasite of
IAO_0000115: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000116: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
IAO_0000117: Chris Mungall
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
has db xref: RO:0002553
has related synonym: epiparasite of
has related synonym: hyperparasitoid of
in subset: ro-eco
shorthand: hyperparasite_of
type: ObjectProperty
sub property of: has host
inverse of: hyperparasitized by

hyperparasitized by
IAO_0000115: inverse of hyperparasite of
IAO_0000117: Chris Mungall
has db xref: RO:0002554
has related synonym: has epiparasite
has related synonym: has hyperparasite
has related synonym: hyperparasitoidized by
in subset: RO_0002259
in subset: ro-eco
shorthand: hyperparasitized_by
type: ObjectProperty
sub property of: host of

allelopath of
IAO_0000117: Chris Mungall
IAO_0000119: http://en.wikipedia.org/wiki/Allelopathy
has db xref: RO:0002555
in subset: ro-eco
shorthand: allelopath_of
type: ObjectProperty
see also: x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y
sub property of: participates in a biotic-biotic interaction with

pathogen of
IAO_0000117: Chris Mungall
has db xref: RO:0002556
in subset: ro-eco
shorthand: pathogen_of
type: ObjectProperty
sub property of: has host
inverse of: has pathogen

has pathogen
IAO_0000117: Chris Mungall
has db xref: RO:0002557
in subset: ro-eco
shorthand: has_pathogen
type: ObjectProperty
sub property of: host of

causally influenced by
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)
has db xref: RO:0002559
shorthand: causally_influenced_by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences

results in movement of
IAO_0000115: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
IAO_0000117: Chris Mungall
has db xref: RO:0002565
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_movement_of
type: ObjectProperty
sub property of: has anatomical participant

causally influences
IAO_0000115: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)
has db xref: RO:0002566
shorthand: causally_influences
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000002
sub property of: causal relation between entities

biomechanically related to
IAO_0000115: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
has db xref: RO:0002567
shorthand: biomechanically_related_to
type: ObjectProperty
domain: CARO_0000003
range: CARO_0000003
sub property of: functionally related to

has muscle antagonist
IAO_0000115: m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Antagonist_(muscle)
has db xref: RO:0002568
shorthand: has_muscle_antagonist
type: ObjectProperty
sub property of: biomechanically related to

has branching part
IAO_0000115: inverse of branching part of
IAO_0000117: Chris Mungall
has db xref: RO:0002569
in subset: RO_0002259
in subset: ro-eco
shorthand: has_branching_part
type: ObjectProperty
sub property of: in branching relationship with

conduit for
IAO_0000115: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
IAO_0000117: Chris Mungall
IAO_0000119: UBERON:cjm
IAO_0000232: This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
has db xref: RO:0002570
in subset: ro-eco
shorthand: conduit_for
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: overlaps

lumen of
IAO_0000115: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:cjm
has db xref: RO:0002571
in subset: ro-eco
shorthand: lumen_of
type: ObjectProperty
range: BFO_0000040
sub property of: BFO_0000050

luminal space of
IAO_0000115: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
IAO_0000117: Chris Mungall
has db xref: RO:0002572
in subset: ro-eco
shorthand: luminal_space_of
type: ObjectProperty
domain: BFO_0000141
sub property of: lumen of

participates in a biotic-biotic interaction with
IAO_0000117: Chris Mungall
has db xref: RO:0002574
in subset: ro-eco
shorthand: participates_in_a_biotic-biotic_interaction_with
type: ObjectProperty
domain: CARO_0001010
range: CARO_0001010
sub property of: biotically interacts with

skeleton of
IAO_0000115: inverse of has skeleton
IAO_0000117: Chris Mungall
has db xref: RO:0002576
in subset: RO_0002259
shorthand: skeleton_of
type: ObjectProperty
domain: CARO_0000003
range: CARO_0000003
sub property of: BFO_0000050

directly regulates
IAO_0000115: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
has db xref: RO:0002578
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: directly_regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of

has part structure that is capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
IAO_0000115: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: Chris Mungall
has db xref: RO:0002584
shorthand: has_part_structure_that_is_capable_of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process

results in closure of
IAO_0000116: p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
has db xref: RO:0002585
shorthand: results_in_closure_of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: has anatomical participant

results in breakdown of
IAO_0000115: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
has db xref: RO:0002586
shorthand: results_in_breakdown_of
type: ObjectProperty
sub property of: has input

results in synthesis of
has db xref: RO:0002587
shorthand: results_in_synthesis_of
type: ObjectProperty
sub property of: results in formation of

results in assembly of
has db xref: RO:0002588
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_assembly_of
type: ObjectProperty
sub property of: results in formation of
sub property of: results in organization of

results in catabolism of
IAO_0000115: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
has db xref: RO:0002589
shorthand: results_in_catabolism_of
type: ObjectProperty
sub property of: results in breakdown of

results in disassembly of
has db xref: RO:0002590
shorthand: results_in_disassembly_of
type: ObjectProperty
sub property of: results in breakdown of
sub property of: results in organization of

results in remodeling of
has db xref: RO:0002591
shorthand: results_in_remodeling_of
type: ObjectProperty
sub property of: has input
sub property of: results in organization of

results in organization of
IAO_0000115: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
has db xref: RO:0002592
shorthand: results_in_organization_of
type: ObjectProperty
sub property of: has anatomical participant

causal relation between material entity and a process
IAO_0000115: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
has db xref: RO:0002595
shorthand: causal_relation_between_material_entity_and_a_process
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000015
sub property of: causally related to

capable of regulating
IAO_0000112: pyrethroid -> growth
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations
has db xref: RO:0002596
shorthand: capable_of_regulating
type: ObjectProperty
sub property of: causal agent in process

capable of negatively regulating
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations
has db xref: RO:0002597
shorthand: capable_of_negatively_regulating
type: ObjectProperty
sub property of: capable of regulating

capable of positively regulating
IAO_0000112: renin -> arteriolar smooth muscle contraction
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations
has db xref: RO:0002598
shorthand: capable_of_positively_regulating
type: ObjectProperty
sub property of: capable of regulating

capable of inhibiting or preventing pathological process
IAO_0000112: pazopanib -> pathological angiogenesis
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
IAO_0000118: treats
IAO_0000119: causal-relations
IAO_0000232: The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
has db xref: RO:0002599
shorthand: capable_of_inhibiting_or_preventing_pathological_process
type: ObjectProperty
sub property of: capable of negatively regulating

capable of upregulating or causing pathological process
IAO_0000112: benzene -> cancer [CHEBI]
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
IAO_0000118: causes disease
IAO_0000119: causal-relations
has db xref: RO:0002600
shorthand: capable_of_upregulating_or_causing_pathological_process
type: ObjectProperty
sub property of: capable of positively regulating

is substance that treats
IAO_0000115: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
IAO_0000118: treats
IAO_0000119: causal-relations
has db xref: RO:0002606
shorthand: is_substance_that_treats
type: ObjectProperty
sub property of: capable of inhibiting or preventing pathological process

process has causal agent
IAO_0000115: Inverse of 'causal agent in process'
IAO_0000119: causal-relations
has db xref: RO:0002608
shorthand: process_has_causal_agent
type: ObjectProperty
sub property of: causally related to

visits
has db xref: RO:0002618
shorthand: visits
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: visited by

visited by
has db xref: RO:0002619
shorthand: visited_by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

visits flowers of
has db xref: RO:0002622
shorthand: visits_flowers_of
type: ObjectProperty
sub property of: visits
inverse of: has flowers visited by

has flowers visited by
has db xref: RO:0002623
shorthand: has_flowers_visited_by
type: ObjectProperty
sub property of: visited by

lays eggs in
has db xref: RO:0002624
shorthand: lays_eggs_in
type: ObjectProperty
sub property of: parasite of
sub property of: visits
inverse of: has eggs laid in by

has eggs laid in by
has db xref: RO:0002625
shorthand: has_eggs_laid_in_by
type: ObjectProperty
sub property of: parasitized by
sub property of: visited by

kills
IAO_0000119: https://github.com/jhpoelen/eol-globi-data/issues/143
has db xref: RO:0002626
shorthand: kills
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: is killed by

is killed by
has db xref: RO:0002627
shorthand: is_killed_by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

directly positively regulates
IAO_0000115: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
has db xref: RO:0002629
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: directly_positively_regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates

directly negatively regulates
IAO_0000115: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates
has db xref: RO:0002630
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: directly_negatively_regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates

ectoparasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
IAO_0000119: Types
has db xref: RO:0002632
shorthand: ectoparasite_of
type: ObjectProperty
sub property of: parasite of
inverse of: has ectoparasite

has ectoparasite
IAO_0000115: inverse of ectoparasite of
has db xref: RO:0002633
in subset: RO_0002259
shorthand: has_ectoparasite
type: ObjectProperty
sub property of: parasitized by

endoparasite of
IAO_0000119: Types
IAO_0000119: A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
has db xref: RO:0002634
has related synonym: lives inside of
shorthand: endoparasite_of
type: ObjectProperty
sub property of: parasite of
inverse of: has endoparasite

has endoparasite
has db xref: RO:0002635
shorthand: has_endoparasite
type: ObjectProperty
sub property of: parasitized by

mesoparasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite
has db xref: RO:0002636
shorthand: mesoparasite_of
type: ObjectProperty
sub property of: parasite of
inverse of: has mesoparasite

has mesoparasite
IAO_0000115: inverse of mesoparasite of
has db xref: RO:0002637
in subset: RO_0002259
shorthand: has_mesoparasite
type: ObjectProperty
sub property of: parasitized by

intercellular endoparasite of
IAO_0000115: A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
IAO_0000119: Types
has db xref: RO:0002638
shorthand: intercellular_endoparasite_of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intercellular endoparasite

has intercellular endoparasite
IAO_0000115: inverse of intercellular endoparasite of
has db xref: RO:0002639
in subset: RO_0002259
shorthand: has_intercellular_endoparasite
type: ObjectProperty
sub property of: has endoparasite

intracellular endoparasite of
IAO_0000115: A sub-relation of endoparasite-of in which the parasite inhabits host cells.
IAO_0000119: Types
has db xref: RO:0002640
shorthand: intracellular_endoparasite_of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intracellular endoparasite

has intracellular endoparasite
IAO_0000115: inverse of intracellular endoparasite of
has db xref: RO:0002641
in subset: RO_0002259
shorthand: has_intracellular_endoparasite
type: ObjectProperty
sub property of: has endoparasite

co-roosts with
IAO_0000115: Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
IAO_0000119: Communal roosting
has db xref: RO:0002801
shorthand: co-roosts_with
type: ObjectProperty
type: SymmetricProperty
sub property of: ecologically co-occurs with

represses expression of
IAO_0000115: Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
IAO_0000117: Vasundra Touré
has db xref: RO:0003002
shorthand: represses_expression_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly negatively regulates activity of

increases expression of
IAO_0000115: Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
IAO_0000117: Vasundra Touré
has db xref: RO:0003003
shorthand: increases_expression_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly positively regulates activity of

causes or contributes to condition
IAO_0000112: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
IAO_0000116: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
has db xref: RO:0003302
shorthand: causes_or_contributes_to_condition
type: ObjectProperty
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
sub property of: causally related to

causes condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
has db xref: RO:0003303
shorthand: causes_condition
type: ObjectProperty
sub property of: causes or contributes to condition

contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
has db xref: RO:0003304
shorthand: contributes_to_condition
type: ObjectProperty
sub property of: causes or contributes to condition

contributes to severity of condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
IAO_0000118: contributes to expressivity of condition
has db xref: RO:0003305
shorthand: contributes_to_severity_of_condition
type: ObjectProperty
sub property of: contributes to condition

contributes to frequency of condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
IAO_0000118: contributes to penetrance of condition
has db xref: RO:0003306
shorthand: contributes_to_frequency_of_condition
type: ObjectProperty
sub property of: contributes to condition

ameliorates condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
IAO_0000118: is preventative for condition
has db xref: RO:0003307
shorthand: ameliorates_condition
type: ObjectProperty
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
sub property of: contributes to severity of condition

exacerbates condition
IAO_0000115: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
has db xref: RO:0003309
shorthand: exacerbates_condition
type: ObjectProperty
sub property of: contributes to severity of condition

condition ameliorated by
IAO_0000115: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
has db xref: RO:0003310
shorthand: condition_ameliorated_by
type: ObjectProperty
sub property of: causally related to

condition exacerbated by
IAO_0000115: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
has db xref: RO:0003311
shorthand: condition_exacerbated_by
type: ObjectProperty
sub property of: causally related to

condition has genetic basis in
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:38:20Z
has db xref: RO:0004000
shorthand: condition_has_genetic_basis_in
type: ObjectProperty
domain: BFO_0000017
range: Class
  union of: BFO_0000015
  union of: BFO_0000019
  union of: BFO_0000040
sub property of: causally related to
inverse of: is genetic basis for condition

has material basis in gain of function germline mutation in
created by: cjm
creation date: 2017-11-05T02:45:20Z
has db xref: RO:0004001
shorthand: has_material_basis_in_gain_of_function_germline_mutation_in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal gain of function germline mutation of in

has material basis in loss of function germline mutation in
created by: cjm
creation date: 2017-11-05T02:45:37Z
has db xref: RO:0004002
shorthand: has_material_basis_in_loss_of_function_germline_mutation_in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal loss of function germline mutation of in

has material basis in germline mutation in
created by: cjm
creation date: 2017-11-05T02:45:54Z
has db xref: RO:0004003
shorthand: has_material_basis_in_germline_mutation_in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation in

has material basis in somatic mutation in
created by: cjm
creation date: 2017-11-05T02:46:07Z
has db xref: RO:0004004
shorthand: has_material_basis_in_somatic_mutation_in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal somatic mutation in

has major susceptibility factor
created by: cjm
creation date: 2017-11-05T02:46:26Z
has db xref: RO:0004005
shorthand: has_major_susceptibility_factor
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal susceptibility factor for

has partial material basis in germline mutation in
created by: cjm
creation date: 2017-11-05T02:46:57Z
has db xref: RO:0004006
shorthand: has_partial_material_basis_in_germline_mutation_in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation partially giving rise to

has primary input or output
IAO_0000115: p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
created by: cjm
creation date: 2018-12-13T11:26:17Z
has db xref: RO:0004007
in subset: valid for go ontology
shorthand: has_primary_input_or_output
type: ObjectProperty
sub property of: RO_0000057

has primary output
IAO_0000115: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
created by: cjm
creation date: 2018-12-13T11:26:32Z
has db xref: RO:0004008
in subset: valid for go ontology
shorthand: has_primary_output
type: ObjectProperty
sub property of: has output
sub property of: has primary input or output

has primary input
IAO_0000115: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
created by: cjm
creation date: 2018-12-13T11:26:56Z
has db xref: RO:0004009
in subset: valid for go ontology
shorthand: has_primary_input
type: ObjectProperty
sub property of: has input
sub property of: has primary input or output

is genetic basis for condition
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:53:08Z
has db xref: RO:0004010
shorthand: is_genetic_basis_for_condition
type: ObjectProperty
range: BFO_0000017
sub property of: is basis for realizable

is causal gain of function germline mutation of in
IAO_0000115: Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:55:51Z
has db xref: RO:0004011
shorthand: is_causal_gain_of_function_germline_mutation_of_in
type: ObjectProperty
sub property of: is genetic basis for condition

is causal loss of function germline mutation of in
IAO_0000115: Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:56:06Z
has db xref: RO:0004012
shorthand: is_causal_loss_of_function_germline_mutation_of_in
type: ObjectProperty
sub property of: is genetic basis for condition

is causal germline mutation in
IAO_0000115: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:56:40Z
has db xref: RO:0004013
shorthand: is_causal_germline_mutation_in
type: ObjectProperty
sub property of: is genetic basis for condition

is causal somatic mutation in
IAO_0000115: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:57:07Z
has db xref: RO:0004014
shorthand: is_causal_somatic_mutation_in
type: ObjectProperty
sub property of: is genetic basis for condition

is causal susceptibility factor for
IAO_0000115: Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:57:43Z
has db xref: RO:0004015
shorthand: is_causal_susceptibility_factor_for
type: ObjectProperty
sub property of: is genetic basis for condition

is causal germline mutation partially giving rise to
IAO_0000115: Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:58:43Z
has db xref: RO:0004016
shorthand: is_causal_germline_mutation_partially_giving_rise_to
type: ObjectProperty
sub property of: is genetic basis for condition

realizable has basis in
created by: cjm
creation date: 2017-11-05T03:20:01Z
has db xref: RO:0004017
shorthand: realizable_has_basis_in
type: ObjectProperty
sub property of: causally related to
inverse of: is basis for realizable

is basis for realizable
created by: cjm
creation date: 2017-11-05T03:20:29Z
has db xref: RO:0004018
shorthand: is_basis_for_realizable
type: ObjectProperty
sub property of: causally related to

disease has basis in
created by: cjm
creation date: 2017-11-05T03:26:47Z
has db xref: RO:0004019
shorthand: disease_has_basis_in
type: ObjectProperty
domain: OGMS_0000031
sub property of: realizable has basis in
sub property of: causal relationship with disease as subject

disease has basis in dysfunction of
IAO_0000115: A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
IAO_0000589: disease has basis in dysfunction of (disease to anatomical structure)
created by: cjm
creation date: 2017-11-05T03:29:32Z
has db xref: RO:0004020
shorthand: disease_has_basis_in_dysfunction_of
type: ObjectProperty
range: CARO_0000006
sub property of: disease has basis in

disease has basis in disruption of
IAO_0000115: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
IAO_0000589: disease has basis in disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:37:52Z
has db xref: RO:0004021
shorthand: disease_has_basis_in_disruption_of
type: ObjectProperty
range: BFO_0000015
sub property of: disease has basis in

disease has basis in feature
IAO_0000115: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
created by: cjm
creation date: 2017-11-05T03:46:07Z
has db xref: RO:0004022
shorthand: disease_has_basis_in_feature
type: ObjectProperty
domain: OGMS_0000031
range: Class
  union of: OGMS_0000031
  union of: UPHENO_0001001
sub property of: has phenotype
sub property of: disease has basis in

causal relationship with disease as subject
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
created by: cjm
creation date: 2017-11-05T03:50:54Z
has db xref: RO:0004023
shorthand: causal_relationship_with_disease_as_subject
type: ObjectProperty
domain: OGMS_0000031
sub property of: causally related to
sub property of: disease relationship

disease causes disruption of
IAO_0000115: A relationship between a disease and a process where the disease process disrupts the execution of the process.
IAO_0000589: disease causes disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:51:09Z
has db xref: RO:0004024
shorthand: disease_causes_disruption_of
type: ObjectProperty
domain: OGMS_0000031
range: BFO_0000015
sub property of: causal relationship with disease as subject

disease causes dysfunction of
IAO_0000589: disease causes dysfunction of (disease to anatomical entity)
created by: cjm
creation date: 2017-11-05T03:58:20Z
has db xref: RO:0004025
shorthand: disease_causes_dysfunction_of
type: ObjectProperty
domain: OGMS_0000031
range: CARO_0000006
sub property of: causal relationship with disease as subject

disease has location
IAO_0000115: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
IAO_0000116: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
IAO_0000232: This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
created by: cjm
creation date: 2017-11-05T04:06:02Z
has db xref: RO:0004026
shorthand: disease_has_location
type: ObjectProperty
domain: OGMS_0000031
range: BFO_0000004
range: Class
  union of: CARO_0000006
  union of: CARO_0000007
sub property of: disease relationship

disease has inflammation site
IAO_0000115: A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
created by: cjm
creation date: 2017-12-26T19:37:31Z
has db xref: RO:0004027
shorthand: disease_has_inflammation_site
type: ObjectProperty
domain: OGMS_0000031
range: BFO_0000004
range: Class
  union of: CARO_0000006
  union of: CARO_0000007
sub property of: disease has location

realized in response to stimulus
IAO_0000115: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: cjm
creation date: 2017-12-26T19:45:49Z
has db xref: RO:0004028
shorthand: realized_in_response_to_stimulus
type: ObjectProperty
domain: BFO_0000017
range: BFO_0000040
sub property of: causally related to

disease has feature
IAO_0000115: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
created by: cjm
creation date: 2017-12-26T19:50:53Z
has db xref: RO:0004029
shorthand: disease_has_feature
type: ObjectProperty
domain: OGMS_0000031
range: Class
  union of: OGMS_0000031
  union of: UPHENO_0001001
sub property of: disease relationship

disease arises from structure
IAO_0000115: A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
created by: cjm
creation date: 2017-12-26T19:58:44Z
has db xref: RO:0004030
shorthand: disease_arises_from_structure
type: ObjectProperty
range: CARO_0000003
sub property of: disease has basis in

enables subfunction
IAO_0000115: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: cjm
creation date: 2018-01-25T23:20:13Z
has db xref: RO:0004031
shorthand: enables_subfunction
type: ObjectProperty
sub property of: functionally related to

acts upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z
has db xref: RO:0004032
in subset: valid for go gp2term
shorthand: acts_upstream_of_or_within,_positive_effect
type: ObjectProperty
sub property of: acts upstream of or within

acts upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z
has db xref: RO:0004033
in subset: valid for go gp2term
shorthand: acts_upstream_of_or_within,_negative_effect
type: ObjectProperty
sub property of: acts upstream of or within

acts upstream of, positive effect
IAO_0000115: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z
has db xref: RO:0004034
in subset: valid for go gp2term
shorthand: acts_upstream_of,_positive_effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect

acts upstream of, negative effect
IAO_0000115: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z
has db xref: RO:0004035
in subset: valid for go gp2term
shorthand: acts_upstream_of,_negative_effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect

causally upstream of or within, negative effect
RO_0004050: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z
has db xref: RO:0004046
shorthand: causally_upstream_of_or_within,_negative_effect
type: ObjectProperty
sub property of: causally upstream of or within

causally upstream of or within, positive effect
RO_0004049: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z
has db xref: RO:0004047
shorthand: causally_upstream_of_or_within,_positive_effect
type: ObjectProperty
sub property of: causally upstream of or within

epiphyte of
IAO_0000115: An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
IAO_0000119: https://en.wikipedia.org/wiki/Epiphyte
has db xref: RO:0008501
shorthand: epiphyte_of
type: ObjectProperty
sub property of: symbiotically interacts with
inverse of: has epiphyte

has epiphyte
IAO_0000115: inverse of epiphyte of
has db xref: RO:0008502
in subset: RO_0002259
shorthand: has_epiphyte
type: ObjectProperty
sub property of: symbiotically interacts with

kleptoparasite of
IAO_0000115: A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
IAO_0000119: https://en.wikipedia.org/wiki/Kleptoparasitism
has db xref: RO:0008503
shorthand: kleptoparasite_of
type: ObjectProperty
sub property of: parasite of
inverse of: kleptoparasitized by

kleptoparasitized by
IAO_0000115: inverse of kleptoparasite of
has db xref: RO:0008504
in subset: RO_0002259
shorthand: kleptoparasitized_by
type: ObjectProperty
sub property of: parasitized by

creates habitat for
IAO_0000115: An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.
has db xref: RO:0008505
shorthand: creates_habitat_for
type: ObjectProperty
domain: CARO_0001010
range: CARO_0001010
sub property of: ecologically related to

ecologically co-occurs with
IAO_0000115: An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.
has db xref: RO:0008506
shorthand: ecologically_co-occurs_with
type: ObjectProperty
type: SymmetricProperty
domain: CARO_0001010
range: CARO_0001010
sub property of: ecologically related to

lays eggs on
IAO_0000115: An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.
has db xref: RO:0008507
shorthand: lays_eggs_on
type: ObjectProperty
sub property of: visits
inverse of: has eggs laid on by

has eggs laid on by
IAO_0000115: inverse of lays eggs on
has db xref: RO:0008508
shorthand: has_eggs_laid_on_by
type: ObjectProperty
sub property of: visited by

realized in response to
IAO_0000112: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
IAO_0000112: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
IAO_0000112: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
IAO_0000115: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: Austin Meier
contributor: Chris Mungall
contributor: David Osumi-Sutherland
contributor: Marie Angelique Laporte
has db xref: RO:0009501
has exact synonym: triggered by process
shorthand: realized_in_response_to
type: ObjectProperty
domain: BFO_0000017
range: BFO_0000015
sub property of: causally related to

regulates activity of
IAO_0000115: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011002
shorthand: regulates_activity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: causally influences

regulates quantity of
IAO_0000115: The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011003
shorthand: regulates_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: causally influences

indirectly regulates activity of
IAO_0000115: The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011004
shorthand: indirectly_regulates_activity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: regulates activity of

decreases by repression quantity of
IAO_0000115: The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011007
shorthand: decreases_by_repression_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: indirectly negatively regulates quantity of

increases by expression quantity of
IAO_0000115: The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011008
shorthand: increases_by_expression_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: indirectly positively regulates quantity of

directly positively regulates quantity of
IAO_0000115: The entity A has an activity that directly positively regulates the quantity of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011009
shorthand: directly_positively_regulates_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly regulates quantity of

directly negatively regulates quantity of
IAO_0000115: The entity A has an activity that directly negatively regulates the quantity of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011010
shorthand: directly_negatively_regulates_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly regulates quantity of

indirectly positively regulates activity of
IAO_0000115: The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
IAO_0000117: Vasundra Touré
IAO_0000118: indirectly activates
has db xref: RO:0011013
shorthand: indirectly_positively_regulates_activity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: indirectly regulates activity of

destabilizes quantity of
IAO_0000112: AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
IAO_0000115: An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
IAO_0000117: Vasundra Touré
has db xref: RO:0011014
shorthand: destabilizes_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly negatively regulates quantity of

stabilizes quantity of
IAO_0000112: AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
IAO_0000115: An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
IAO_0000117: Vasundra Touré
has db xref: RO:0011015
shorthand: stabilizes_quantity_of
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
sub property of: directly positively regulates quantity of

indirectly negatively regulates activity of
IAO_0000115: The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
IAO_0000117: Vasundra Touré
IAO_0000118: indirectly inhibits
has db xref: RO:0011016
shorthand: indirectly_negatively_regulates_activity_of
type: ObjectProperty
sub property of: indirectly regulates activity of

directly regulates quantity of
IAO_0000115: The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011021
shorthand: directly_regulates_quantity_of
type: ObjectProperty
sub property of: regulates quantity of

indirectly regulates quantity of
IAO_0000115: The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011022
shorthand: indirectly_regulates_quantity_of
type: ObjectProperty
sub property of: regulates quantity of

indirectly negatively regulates quantity of
IAO_0000115: The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011023
shorthand: indirectly_negatively_regulates_quantity_of
type: ObjectProperty
sub property of: indirectly regulates quantity of

indirectly positively regulates quantity of
IAO_0000115: The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
IAO_0000117: Vasundra Touré
has db xref: RO:0011024
shorthand: indirectly_positively_regulates_quantity_of
type: ObjectProperty
sub property of: indirectly regulates quantity of

has small molecule regulator
IAO_0000115: a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
created by: pg
creation date: 2020-04-22T20:27:26Z
has db xref: RO:0012000
shorthand: has_small_molecule_regulator
type: ObjectProperty
sub property of: RO_0000057

has small molecule activator
IAO_0000115: a relation between a process and a continuant, in which the process is activated by the small molecule continuant
created by: pg
creation date: 2020-04-22T20:28:37Z
has db xref: RO:0012001
shorthand: has_small_molecule_activator
type: ObjectProperty
sub property of: has small molecule regulator

has small molecule inhibitor
IAO_0000115: a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
created by: pg
creation date: 2020-04-22T20:28:54Z
has db xref: RO:0012002
shorthand: has_small_molecule_inhibitor
type: ObjectProperty
sub property of: has small molecule regulator

acts on population of
IAO_0000115: p acts on population of c iff c' is a collection, has members of type c, and p has participant c
created by: pg
creation date: 2020-06-08T17:21:33Z
has db xref: RO:0012003
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: acts_on_population_of
type: ObjectProperty
sub property of: RO_0000057

is small molecule regulator
IAO_0000115: a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
created by: pg
creation date: 2020-06-24T13:15:17Z
has db xref: RO:0012004
shorthand: is_small_molecule_regulator
type: ObjectProperty
sub property of: RO_0000057

is small molecule activator
IAO_0000115: a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
created by: pg
creation date: 2020-06-24T13:15:26Z
has db xref: RO:0012005
shorthand: is_small_molecule_activator
type: ObjectProperty
sub property of: is small molecule regulator

is small molecule inhibitor
IAO_0000115: a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
created by: pg
creation date: 2020-06-24T13:15:35Z
has db xref: RO:0012006
shorthand: is_small_molecule_inhibitor
type: ObjectProperty
sub property of: is small molecule regulator

results in adhesion of
IAO_0000115: The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.
created by: pg
creation date: 2020-08-27T08:13:59Z
has db xref: RO:0012007
shorthand: results_in_adhesion_of
type: ObjectProperty
sub property of: has anatomical participant

results in fusion of
created by: pg
creation date: 2021-02-26T07:28:29Z
has db xref: RO:0012008
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: results_in_fusion_of
type: ObjectProperty
sub property of: results in organization of

has synaptic IO in
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:26:52Z
has db xref: RO:0013001
has exact synonym: has synaptic input or output in
shorthand: has_synaptic_IO_in
type: ObjectProperty
sub property of: has synaptic terminal in

receives synaptic input in
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:42:23Z
has db xref: RO:0013002
shorthand: receives_synaptic_input_in
type: ObjectProperty
sub property of: has postsynaptic terminal in
sub property of: has synaptic IO in

sends synaptic output to
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:45:06Z
has db xref: RO:0013003
shorthand: sends_synaptic_output_to
type: ObjectProperty
sub property of: has presynaptic terminal in
sub property of: has synaptic IO in

has synaptic IO throughout
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:52:19Z
has db xref: RO:0013004
shorthand: has_synaptic_IO_throughout
type: ObjectProperty
sub property of: has synaptic IO in

receives synaptic input throughout
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:55:36Z
has db xref: RO:0013005
shorthand: receives_synaptic_input_throughout
type: ObjectProperty
sub property of: receives synaptic input in
sub property of: has synaptic IO throughout

sends synaptic output throughout
IAO_0000115: A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:57:27Z
has db xref: RO:0013006
shorthand: sends_synaptic_output_throughout
type: ObjectProperty
sub property of: sends synaptic output to
sub property of: has synaptic IO throughout

has sensory dendrite in
IAO_0000115: Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-20T12:10:09Z
has db xref: RO:0013007
has exact synonym: has sensory dendrite location
has exact synonym: has sensory terminal in
has exact synonym: has sensory terminal location
shorthand: has_sensory_dendrite_in
type: ObjectProperty
domain: CL_0000101
sub property of: has dendrite location

disease has infectious agent
IAO_0000115: A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.
created by: http://orcid.org/0000-0001-5208-3432
has db xref: RO:0014001
shorthand: disease_has_infectious_agent
type: ObjectProperty
sub property of: disease has basis in

disease relationship
IAO_0000115: This relation groups relations between diseases and any other kind of entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
created by: cjm
creation date: 2018-09-26T00:00:32Z
has db xref: RO:0040035
shorthand: disease_relationship
type: ObjectProperty

has anatomical participant
IAO_0000115: p has anatomical participant c iff p has participant c, and c is an anatomical entity
created by: cjm
creation date: 2018-09-26T01:08:58Z
has db xref: RO:0040036
shorthand: has_anatomical_participant
type: ObjectProperty
range: Class
  union of: CARO_0000006
  union of: CARO_0000007
sub property of: RO_0000057

Axiom
has db xref: GOC:dos
annotated property: comment
annotated source: directly regulated by
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
has db xref: GOC:dos
annotated property: IAO_0000115
annotated source: directly negatively regulated by
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.

Axiom
has db xref: GOC:dos
annotated property: IAO_0000115
annotated source: directly positively regulated by
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.

Axiom
has db xref: GOC:dos
annotated property: IAO_0000115
annotated source: has effector activity
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.

Axiom
has db xref: GOC:dos
annotated property: IAO_0000115
annotated source: in register with
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.

Axiom
annotated property: IAO_0000112
annotated source: adjacent to
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

Axiom
comment: We need to import uberon muscle to create a stricter domain constraint
annotated property: domain
annotated source: has muscle origin
annotated target: CARO_0000003

Axiom
IAO_0000116: We need to import uberon muscle into RO to use as a stricter domain constraint
annotated property: domain
annotated source: has muscle insertion
annotated target: CARO_0000003

Axiom
has db xref: GOC:cjm
has db xref: GOC:dos
annotated property: IAO_0000115
annotated source: is active in
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.

Axiom
IAO_0000116: This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
annotated property: range
annotated source: has skeleton
annotated target: CARO_0000006

Axiom
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
annotated property: IAO_0000118
annotated source: capable of inhibiting or preventing pathological process
annotated target: treats

Axiom
has db xref: GOC:cjm
has db xref: GOC:dph
has db xref: GOC:kva
has db xref: GOC:pt
comment: PMID:27812932
annotated property: IAO_0000115
annotated source: has primary output
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.

Axiom
has db xref: GOC:cjm
has db xref: GOC:dph
has db xref: GOC:kva
has db xref: GOC:pt
comment: PMID:27812932
annotated property: IAO_0000115
annotated source: has primary input
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.

Axiom
has db xref: RO:cjm
annotated property: hasExactSynonym
annotated source: realized in response to
annotated target: triggered by process