fbbi.owl
type: Ontology
version IRI: fbbi.owl
default-namespace: image
has_obo_format_version: 1.2
comment: Biological Imaging Methods CV
comment: This CV covers sample preparation, visualization and imaging methods.
comment: corrections and additions to chris@bio.umass.edu
comment: editor:Chris Woodcock (The Cell: An Image Library)

definition
type: AnnotationProperty
IAO_0000114: IAO_0000122

OBO foundry unique label
type: AnnotationProperty
IAO_0000114: IAO_0000125

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

PhenoImageShare ImagingMethod
type: AnnotationProperty
comment: A small set of imaging methods for use in PhenoImageShare indexes
sub property of: subset_property

subset_property
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: BFO_0000017
RO_0040042: BFO_0000019
RO_0040042: BFO_0000020
RO_0040042: BFO_0000031

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
RO_0001900: RO_0001901

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
IAO_0000111: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
IAO_0000118: occurs_in
IAO_0000118: unfolds in
IAO_0000118: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
IAO_0000111: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

makes_use_of
type: ObjectProperty
type: TransitiveProperty
definition: The child is an essential component of the parent device, or plays an essential role in performance of the parent function.
created by: jm
creation date: 2010-03-09T09:32:04Z
has_obo_namespace: image
id: FBbi:00000346

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: 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 negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: 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
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'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: 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
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'.

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

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: 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

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
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.

Axiom
annotated source: directly regulated by
annotated property: comment
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.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: 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

Axiom
annotated source: directly negatively regulated by
annotated property: definition
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.
database_cross_reference: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: 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

Axiom
annotated source: directly positively regulated by
annotated property: definition
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.
database_cross_reference: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: 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
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
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.
database_cross_reference: GOC:dos

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part
IAO_0000114: IAO_0000125
definition: 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
in_subset: ro-eco

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: IAO_0000125
definition: 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
in_subset: ro-eco

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
IAO_0000114: IAO_0000125
definition: 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
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: IAO_0000125
definition: inverse of develops from
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
in_subset: RO_0002259

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
IAO_0000114: IAO_0000125
definition: 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.
OBO foundry unique label: regulates (processual)
IAO_0000600: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: 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
OBO foundry unique label: negatively regulates (process to process)
RO_0004050: regulates

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: 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
OBO foundry unique label: positively regulates (process to process)
RO_0004049: regulates

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
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'
definition: 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)".
IAO_0000424: RO_0000053 some (RO_0000054 only ?Y)
in_subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: 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
IAO_0000424: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000119: Allen's interval algebra
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
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
range: material entity
IAO_0000114: IAO_0000125
definition: 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
in_subset: ro-eco

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops 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
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: Chris Mungall

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: inverse of has developmental contribution from
IAO_0000117: Chris Mungall
in_subset: RO_0002259

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
IAO_0000114: IAO_0000125
definition: 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
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally 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.
definition: 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.

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally 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.
definition: 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_related_synonym: affects

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000125
definition: Inverse of developmentally preceded by
IAO_0000117: Chris Mungall

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
RO_0004049: causally upstream of
creator: cjm
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

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
RO_0004050: causally upstream of
creator: cjm
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

mereotopologically related to
type: ObjectProperty
definition: 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

developmentally related to
type: ObjectProperty
definition: 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

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
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.

functionally related to
type: ObjectProperty
definition: 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

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: 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

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: 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

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
IAO_0000117: Chris Mungall

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
IAO_0000117: Chris Mungall
OBO foundry unique label: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: Chris Mungall
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: Chris Mungall
in_subset: RO_0002259

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
IAO_0000117: Chris Mungall
in_subset: RO_0002259
in_subset: ro-eco

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
IAO_0000114: IAO_0000428
definition: 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 potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: 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 potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: 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 potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: IAO_0000428
definition: 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

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: IAO_0000428
definition: inverse of upstream of
IAO_0000117: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall

causally related to
type: ObjectProperty
IAO_0000114: IAO_0000428
definition: 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.

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
IAO_0000114: IAO_0000428
definition: 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

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
IAO_0000114: IAO_0000428
definition: 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

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: 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_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
in_subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: 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

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: 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

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
definition: 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

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
definition: 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_exact_synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: definition
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.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dos

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: 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_exact_synonym: in pairwise interaction with
in_subset: ro-eco

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: 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

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
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.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: 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_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: 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_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: 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_exact_synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: 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
in_subset: ro-eco

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has part
annotated target: occurs in
is a defining property chain axiom: true

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: Chris Mungall

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: 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

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: 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.

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
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.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
OBO foundry unique label: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: 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
OBO foundry unique label: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: 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
OBO foundry unique label: directly regulates (processual)
RO_0002575: regulates

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
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: 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

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: 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

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: 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

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
definition: 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

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: 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
OBO foundry unique label: directly positively regulates (process to process)
RO_0004049: directly regulates

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: 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
OBO foundry unique label: directly negatively regulates (process to process)
RO_0004050: directly regulates

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: 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

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: 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

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: 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

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: 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

continuant
type: Class
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

occurrent
type: Class
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
definition: An entity that has temporal parts and that happens, unfolds or develops through time.

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

process
type: Class
subclass of: occurrent
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

anatomical entity
type: Class
subclass of: biological entity
IAO_0000412: caro.owl

biological entity
type: Class
subclass of: independent continuant

dummy term
type: Class
subclass of: Thing
created by: jm
creation date: 2010-03-07T02:05:26Z
has_obo_namespace: image
id: FBbi:00000000
deprecated: true

sample preparation method
type: Class
subclass of: method involved in biological imaging
has_obo_namespace: image
id: FBbi:00000001

chemically fixed tissue
type: Class
subclass of: fixation method
has_obo_namespace: image
id: FBbi:00000002

coagulating-fixative fixed tissue
type: Class
subclass of: chemically fixed tissue
subclass of: solvent permeabilized
has_obo_namespace: image
id: FBbi:00000003

acetone fixed tissue
type: Class
subclass of: coagulating-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000004

acrolein fixed tissue
type: Class
subclass of: coagulating-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000005

ethanol fixed tissue
type: Class
subclass of: coagulating-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000006

methanol fixed tissue
type: Class
subclass of: coagulating-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000007

crosslinking-fixative fixed tissue
type: Class
subclass of: chemically fixed tissue
has_obo_namespace: image
id: FBbi:00000008

ethylene glycol-bis-succinimidyl succinate fixed tissue
type: Class
subclass of: crosslinking-fixative fixed tissue
has_obo_namespace: image
has_related_synonym: EGS
id: FBbi:00000009

formaldehyde fixed tissue
type: Class
subclass of: crosslinking-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000010

glutaraldehyde fixed tissue
type: Class
subclass of: crosslinking-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000011

osmium tetroxide fixed tissue
type: Class
subclass of: crosslinking-fixative fixed tissue
has_obo_namespace: image
id: FBbi:00000012

cryofixed tissue
type: Class
subclass of: fixation method
has_obo_namespace: image
id: FBbi:00000013

unfixed tissue
type: Class
subclass of: fixation method
has_obo_namespace: image
id: FBbi:00000014

embedded tissue
type: Class
subclass of: sample preparation method
disjoint with: unembedded tissue
has_obo_namespace: image
id: FBbi:00000015

tissue in plastic embedment
type: Class
subclass of: embedded tissue
has_obo_namespace: image
id: FBbi:00000016

tissue in acrylic resin embedment
type: Class
subclass of: tissue in plastic embedment
has_obo_namespace: image
id: FBbi:00000017

tissue in epoxy resin embedment
type: Class
subclass of: tissue in plastic embedment
has_obo_namespace: image
id: FBbi:00000018

tissue in wax embedment
type: Class
subclass of: embedded tissue
has_obo_namespace: image
id: FBbi:00000019

tissue in paraffin embedment
type: Class
subclass of: tissue in wax embedment
has_obo_namespace: image
id: FBbi:00000020

tissue in polyester wax embedment
type: Class
subclass of: tissue in wax embedment
has_obo_namespace: image
id: FBbi:00000021

tissue in polyethylene glycol embedment
type: Class
subclass of: tissue in wax embedment
has_obo_namespace: image
id: FBbi:00000022

unembedded tissue
type: Class
subclass of: sample preparation method
has_obo_namespace: image
id: FBbi:00000023

whole mounted tissue
type: Class
subclass of: sample preparation method
disjoint with: sectioned tissue
has_obo_namespace: image
id: FBbi:00000024

living tissue
type: Class
subclass of: unfixed tissue
definition: Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state.
has_obo_namespace: image
has_related_synonym: live-cell imaging
id: FBbi:00000025

Axiom
annotated source: living tissue
annotated property: definition
annotated target: Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state.
database_cross_reference: XX:ISBN978-087969683-2

sectioned tissue
type: Class
subclass of: sample preparation method
has_obo_namespace: image
id: FBbi:00000026

cryostat-sectioned tissue
type: Class
subclass of: sectioned tissue
has_obo_namespace: image
id: FBbi:00000027

hand-sectioned tissue
type: Class
subclass of: sectioned tissue
has_obo_namespace: image
id: FBbi:00000028

microtome-sectioned tissue
type: Class
subclass of: sectioned tissue
has_obo_namespace: image
id: FBbi:00000029

vibratome-sectioned tissue
type: Class
subclass of: sectioned tissue
has_obo_namespace: image
id: FBbi:00000030

visualization method
type: Class
subclass of: method involved in biological imaging
has_obo_namespace: image
id: FBbi:00000031

endogenous substrate, non-vital dye
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000032
deprecated: true

diagram
type: Class
subclass of: portrayed image
has_obo_namespace: image
id: FBbi:00000033

HA peptide tag
type: Class
subclass of: small genetically encoded tag
OBO foundry unique label: visualization of HA peptide tag
has_obo_namespace: image
id: FBbi:00000034

cresyl fast violet
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of cresyl fast violet
has_obo_namespace: image
id: FBbi:00000035

endogenous substrate, diaminobenzidine
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000036
deprecated: true

eosin
type: Class
subclass of: non-specific protein affinity
definition: Staining with an aqueous or alcoholic solution of eosin Y,colors eosinophilic structures in various shades of red, pink and orange. The eosinophilic structures are generally composed of intracellular or extracellular protein. The Lewy bodies and Mallory bodies are examples of eosinophilic structures. Most of the cytoplasm is eosinophilic. Red blood cells are stained intensely red.
OBO foundry unique label: visualization of eosin
has_obo_namespace: image
id: FBbi:00000037

Axiom
annotated source: eosin
annotated property: definition
annotated target: Staining with an aqueous or alcoholic solution of eosin Y,colors eosinophilic structures in various shades of red, pink and orange. The eosinophilic structures are generally composed of intracellular or extracellular protein. The Lewy bodies and Mallory bodies are examples of eosinophilic structures. Most of the cytoplasm is eosinophilic. Red blood cells are stained intensely red.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/H%26E_stain

ethidium bromide
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of ethidium bromide
has_obo_namespace: image
id: FBbi:00000038

fuchsin
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of fuchsin
has_obo_namespace: image
id: FBbi:00000039

giemsa
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of giemsa
has_obo_namespace: image
id: FBbi:00000040

hematoxylin
type: Class
subclass of: non-specific protein affinity
definition: The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The staining of nuclei by hemalum does not require the presence of DNA and is probably due to binding of the dye-metal complex to arginine-rich basic nucleoproteins such as histones. The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes is prevented by chemical or enzymatic extraction of nucleic acids. Such extractions do not prevent staining of nuclei by hemalum.
OBO foundry unique label: visualization of hematoxylin
has_obo_namespace: image
id: FBbi:00000041

Axiom
annotated source: hematoxylin
annotated property: definition
annotated target: The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The staining of nuclei by hemalum does not require the presence of DNA and is probably due to binding of the dye-metal complex to arginine-rich basic nucleoproteins such as histones. The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes is prevented by chemical or enzymatic extraction of nucleic acids. Such extractions do not prevent staining of nuclei by hemalum.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/H%26E_stain

methyl green
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of methyl green
has_obo_namespace: image
id: FBbi:00000042

methyl violet
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of methyl violet
has_obo_namespace: image
id: FBbi:00000043

nitro blue tetrazolium chloride
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of nitro blue tetrazolium chloride
has_obo_namespace: image
id: FBbi:00000044

nuclear fast red
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of nuclear fast red
has_obo_namespace: image
id: FBbi:00000045

orcein
type: Class
subclass of: non-specific protein affinity
OBO foundry unique label: visualization of orcein
has_obo_namespace: image
id: FBbi:00000046

propidium iodide
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of propidium iodide
has_obo_namespace: image
has_related_synonym: PI
id: FBbi:00000047

SYTOX Green
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of SYTOX Green
has_obo_namespace: image
id: FBbi:00000048

toluidine blue
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of toluidine blue
has_obo_namespace: image
id: FBbi:00000049

endogenous substrate, vital dye
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000050
deprecated: true

acridine orange
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of acridine orange
has_obo_namespace: image
has_related_synonym: AO
id: FBbi:00000051

Hoechst 33342
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of Hoechst 33342
has_obo_namespace: image
has_related_synonym: HO342
has_related_synonym: Hoechst 33342
id: FBbi:00000052

cationic colloidal gold
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of cationic colloidal gold
has_obo_namespace: image
id: FBbi:00000053

CMX rosamine (Mitotracker Red)
type: Class
subclass of: probe for mitochondria
OBO foundry unique label: visualization of CMX rosamine (Mitotracker Red)
has_obo_namespace: image
has_related_synonym: Mitotracker X
id: FBbi:00000054

DiOC6 (3,3'-dihexyloxacarbocyanine iodide)
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiOC6 (3,3'-dihexyloxacarbocyanine iodide)
has_obo_namespace: image
has_related_synonym: DiOC
id: FBbi:00000055

4',6-diamidino-2-phenylindole (DAPI)
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of 4',6-diamidino-2-phenylindole (DAPI)
has_obo_namespace: image
has_related_synonym: DAPI
id: FBbi:00000056

lucifer yellow
type: Class
subclass of: miscellaneous fill
has_obo_namespace: image
id: FBbi:00000057

methylene blue
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of methylene blue
has_obo_namespace: image
id: FBbi:00000058

Nile blue A
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of Nile blue A
has_obo_namespace: image
id: FBbi:00000059

Nile red
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of Nile red
has_obo_namespace: image
id: FBbi:00000060

pyronine
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of pyronine
has_obo_namespace: image
id: FBbi:00000061

rhodamine 123
type: Class
subclass of: probe for mitochondria
OBO foundry unique label: visualization of rhodamine 123
has_obo_namespace: image
id: FBbi:00000062

rhodamine B
type: Class
subclass of: optically-dense stain
OBO foundry unique label: visualization of rhodamine B
has_obo_namespace: image
id: FBbi:00000063

SYTO Blue
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of SYTO Blue
has_obo_namespace: image
id: FBbi:00000064

SYTO Green
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of SYTO Green
has_obo_namespace: image
id: FBbi:00000065

SYTO Orange
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of SYTO Orange
has_obo_namespace: image
id: FBbi:00000066

SYTO Red
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of SYTO Red
has_obo_namespace: image
id: FBbi:00000067

YO-PRO-1
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of YO-PRO-1
has_obo_namespace: image
id: FBbi:00000068

endogenous substrate, dye conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000069
deprecated: true

endogenous substrate, acidotropic-fluor conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: LysoTracker
id: FBbi:00000070
deprecated: true

endogenous substrate, lectin-fluor conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000071
deprecated: true

endogenous substrate, lectin-gold conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000072
deprecated: true

taxol
type: Class
subclass of: affinity for specific proteins
OBO foundry unique label: visualization of taxol
has_obo_namespace: image
id: FBbi:00000073

endogenous substrate, phalloidin-fluor conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000074
deprecated: true

exogenous label
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000075
deprecated: true

genetically encoded enzyme
type: Class
subclass of: genetically encoded tag
OBO foundry unique label: visualization of genetically encoded enzyme
has_obo_namespace: image
id: FBbi:00000076

beta-galactosidase
type: Class
subclass of: genetically encoded enzyme
OBO foundry unique label: visualization of beta-galactosidase
has_obo_namespace: image
has_related_synonym: lacZ, X-gal
id: FBbi:00000077

beta-glucuronidase
type: Class
subclass of: genetically encoded enzyme
OBO foundry unique label: visualization of beta-glucuronidase
has_obo_namespace: image
has_related_synonym: GUS, X-gluc
id: FBbi:00000078

genetically encoded tag
type: Class
subclass of: macromolecular probe
OBO foundry unique label: visualization of genetically encoded tag
has_obo_namespace: image
id: FBbi:00000079

EBFP
type: Class
subclass of: Blue fluorescent protein from Aequorea victoria
OBO foundry unique label: visualization of EBFP
has_obo_namespace: image
has_related_synonym: BFP
id: FBbi:00000080

ECFP
type: Class
subclass of: Cyan fluorescent protein from Aequorea
OBO foundry unique label: visualization of ECFP
has_obo_namespace: image
has_related_synonym: CFP
id: FBbi:00000081

EGFP
type: Class
subclass of: Green fluorescent protein from Aequorea
OBO foundry unique label: visualization of EGFP
has_obo_namespace: image
has_related_synonym: GFP
id: FBbi:00000082

Aequorea victoria red fluorescent protein tag
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: RFP
id: FBbi:00000083
deprecated: true

EYFP
type: Class
subclass of: Yellow fluorescent protein from Aequorea
OBO foundry unique label: visualization of EYFP
has_obo_namespace: image
has_related_synonym: YFP
id: FBbi:00000084

DsRed
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of DsRed
has_obo_namespace: image
has_related_synonym: DsRed
id: FBbi:00000085

c-MYC peptide tag
type: Class
subclass of: small genetically encoded tag
OBO foundry unique label: visualization of c-MYC peptide tag
has_obo_namespace: image
id: FBbi:00000086

FLAG peptide tag
type: Class
subclass of: small genetically encoded tag
OBO foundry unique label: visualization of FLAG peptide tag
has_obo_namespace: image
id: FBbi:00000087

intracellular filling
type: Class
subclass of: visualization of contiguous regions
definition: visualization of the connected regions of a cell by filling with a label
has_obo_namespace: image
id: FBbi:00000088

tissue in vitreous ice embedment
type: Class
subclass of: embedded tissue
definition: Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C
created by: jm
creation date: 2010-03-07T02:05:48Z
has_obo_namespace: image
has_related_synonym: tissue in amorphous ice embedment
id: FBbi:00000089

Axiom
annotated source: tissue in vitreous ice embedment
annotated property: definition
annotated target: Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C
database_cross_reference: PMID:3043536

fluor labeled RNA fill
type: Class
subclass of: intracellular filling
has_obo_namespace: image
id: FBbi:00000090

5-SFX fluorescein RNA fill
type: Class
subclass of: fluor labeled RNA fill
has_obo_namespace: image
id: FBbi:00000091

X-rhodamine RNA fill
type: Class
subclass of: fluor labeled RNA fill
has_obo_namespace: image
id: FBbi:00000092

permeabilized tissue
type: Class
subclass of: sample preparation method
definition: Tissue treated to make cell membranes permeable, typically for the purpose of allowing access by exogenous stains or substrates.
created by: jm
creation date: 2010-03-07T02:26:37Z
has_obo_namespace: image
id: FBbi:00000093

fluor labeled protein fill
type: Class
subclass of: intracellular filling
has_obo_namespace: image
id: FBbi:00000094

fluor conjugated actin fill
type: Class
subclass of: fluor labeled protein fill
has_obo_namespace: image
id: FBbi:00000095

Alexa Fluor 488 actin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000096
deprecated: true

Alexa Fluor 568 actin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000097
deprecated: true

fluoresceine actin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000098
deprecated: true

rhodamine actin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000099
deprecated: true

phalloidin
type: Class
subclass of: affinity for specific proteins
OBO foundry unique label: visualization of phalloidin
has_obo_namespace: image
id: FBbi:00000100

Alexa Fluor 350 phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000101
deprecated: true

Alexa Fluor 488 phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000102
deprecated: true

eosin phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000103
deprecated: true

fluoresceine phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000104
deprecated: true

Oregon Green 488 phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000105
deprecated: true

Oregon Green 514 phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000106
deprecated: true

rhodamine phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000107
deprecated: true

Texas Red-X phalloidin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000108
deprecated: true

fluor conjugated tubulin fill
type: Class
subclass of: fluor labeled protein fill
has_obo_namespace: image
id: FBbi:00000109

Oregon Green 514 tubulin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000110
deprecated: true

X-rhodamine tubulin fill
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000111
deprecated: true

probe for lipid
type: Class
subclass of: small-molecule probe
OBO foundry unique label: visualization of probe for lipid
has_obo_namespace: image
id: FBbi:00000112

DiA
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiA
has_obo_namespace: image
id: FBbi:00000113

DiD
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiD
has_obo_namespace: image
id: FBbi:00000114

DiI
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiI
has_obo_namespace: image
id: FBbi:00000115

DiO
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiO
has_obo_namespace: image
id: FBbi:00000116

DiR
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiR
has_obo_namespace: image
id: FBbi:00000117

miscellaneous fill
type: Class
subclass of: intracellular filling
has_obo_namespace: image
id: FBbi:00000118

biotin ethylenediamine fill
type: Class
subclass of: miscellaneous fill
has_obo_namespace: image
has_related_synonym: Neurobiotin
id: FBbi:00000119

cobalt fill
type: Class
subclass of: miscellaneous fill
has_obo_namespace: image
id: FBbi:00000120

silver-intensified cobalt fill
type: Class
subclass of: cobalt fill
has_obo_namespace: image
id: FBbi:00000121

metabolically incorporated radioisotope
type: Class
subclass of: visualization by chemical attribute
OBO foundry unique label: visualization of metabolically incorporated radioisotope
has_obo_namespace: image
id: FBbi:00000122

[14]C
type: Class
subclass of: metabolically incorporated radioisotope
OBO foundry unique label: visualization of metabolically incorporated [14]C
has_obo_namespace: image
id: FBbi:00000123

[32]P
type: Class
subclass of: metabolically incorporated radioisotope
OBO foundry unique label: visualization of metabolically incorporated [32]P
has_obo_namespace: image
id: FBbi:00000124

[33]P
type: Class
subclass of: metabolically incorporated radioisotope
OBO foundry unique label: visualization of metabolically incorporated [33]P
has_obo_namespace: image
id: FBbi:00000125

[35]S
type: Class
subclass of: metabolically incorporated radioisotope
OBO foundry unique label: visualization of metabolically incorporated [35]S
has_obo_namespace: image
id: FBbi:00000126

[3]H
type: Class
subclass of: metabolically incorporated radioisotope
OBO foundry unique label: visualization of metabolically incorporated [3]H
has_obo_namespace: image
id: FBbi:00000127

vizualization of label conjugated to probe
type: Class
subclass of: visualization method
has_obo_namespace: image
id: FBbi:00000128

glycerol permeabilized
type: Class
subclass of: permeabilized tissue
definition: tissue made permeable by the action of glycerol
created by: jm
creation date: 2010-03-07T02:37:12Z
has_obo_namespace: image
has_related_synonym: glycerinated tissue
id: FBbi:00000129

labeled primary antibody
type: Class
subclass of: antibody
OBO foundry unique label: visualization of labeled primary antibody
has_obo_namespace: image
id: FBbi:00000130

primary antibody-enzyme conjugate, substrate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000131
deprecated: true

alkaline phosphatase
type: Class
subclass of: enzyme label
OBO foundry unique label: visualization of alkaline phosphatase conjugated to probe
has_obo_namespace: image
id: FBbi:00000132

primary antibody-alkaline phosphastase conjugate, DAB
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000133
deprecated: true

primary antibody-alkaline phosphastase conjugate, ELF 97 phosphate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000134
deprecated: true

primary antibody-alkaline phosphastase conjugate, Vector Black
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000135
deprecated: true

primary antibody-alkaline phosphastase conjugate, Vector Blue
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000136
deprecated: true

primary antibody-alkaline phosphastase conjugate, Vector Red
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000137
deprecated: true

horseradish peroxidase
type: Class
subclass of: enzyme label
OBO foundry unique label: visualization of horseradish peroxidase conjugated to probe
has_obo_namespace: image
id: FBbi:00000138

primary antibody-horseradish peroxidase, 4-chloro-1-naphthol
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000139
deprecated: true

primary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000140
deprecated: true

primary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000141
deprecated: true

primary antibody-horseradish peroxidase, Vector NovaRed
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000142
deprecated: true

primary antibody-horseradish peroxidase, Vector SG
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000143
deprecated: true

primary antibody-horseradish peroxidase, Vector VIP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000144
deprecated: true

primary antibody-fluor conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000145
deprecated: true

primary antibody-aminomethylcoumarin acetate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: AMCA
id: FBbi:00000146
deprecated: true

primary antibody-Cascade blue
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000147
deprecated: true

primary antibody-cyanine
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: Cy2
id: FBbi:00000148
deprecated: true

primary antibody-fluorescein isothiocyanate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: FITC
id: FBbi:00000149
deprecated: true

primary antibody-indocarbocyanine
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: Cy3
id: FBbi:00000150
deprecated: true

primary antibody-indodicarbocyanine
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: Cy5
id: FBbi:00000151
deprecated: true

primary antibody-rhodamine red-X
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: RRX
id: FBbi:00000152
deprecated: true

primary antibody-tetramethyl rhodamine isothiocyanate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: TRITC
id: FBbi:00000153
deprecated: true

primary antibody-Texas Red
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: TR
id: FBbi:00000154
deprecated: true

primary antibody-gold conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000155
deprecated: true

primary antibody plus labeled secondary antibody
type: Class
subclass of: antibody
OBO foundry unique label: visualization of primary antibody plus labeled secondary antibody
has_obo_namespace: image
id: FBbi:00000156

secondary antibody-enzyme conjugate, substrate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000157
deprecated: true

acid phosphatase
type: Class
subclass of: enzyme label
OBO foundry unique label: visualization of acid phosphatase conjugated to probe
has_obo_namespace: image
id: FBbi:00000158

secondary antibody-alkaline phosphastase conjugate, DAB
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000159
deprecated: true

secondary antibody-alkaline phosphastase conjugate, ELF 97 phosphate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000160
deprecated: true

secondary antibody-alkaline phosphastase conjugate, Fast Blue B
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000161
deprecated: true

secondary antibody-alkaline phosphastase conjugate, Fast Red
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000162
deprecated: true

secondary antibody-alkaline phosphastase conjugate, INT
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000163
deprecated: true

secondary antibody-alkaline phosphastase conjugate, Magenta Phos
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000164
deprecated: true

secondary antibody-alkaline phosphastase conjugate, NABP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000165
deprecated: true

secondary antibody-alkaline phosphastase conjugate, NAGP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000166
deprecated: true

secondary antibody-alkaline phosphastase conjugate, NAMP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000167
deprecated: true

secondary antibody-alkaline phosphastase conjugate, NATP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000168
deprecated: true

secondary antibody-alkaline phosphastase conjugate, NBT
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000169
deprecated: true

secondary antibody-alkaline phosphastase conjugate, Vector Black
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000170
deprecated: true

secondary antibody-alkaline phosphastase conjugate, Vector Blue
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000171
deprecated: true

secondary antibody-alkaline phosphastase conjugate, Vector Red
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000172
deprecated: true

secondary antibody-alkaline phosphastase conjugate, BCIP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000173
deprecated: true

secondary antibody-beta-galactosidase, X-Gal
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000174
deprecated: true

secondary antibody-beta-glucuronidase, X-gluc
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000175
deprecated: true

esterase
type: Class
subclass of: enzyme label
OBO foundry unique label: visualization of esterase conjugated to probe
has_obo_namespace: image
id: FBbi:00000176

secondary antibody-esterase, Naphthol-AS-D-chloroacetate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000177
deprecated: true

glucose oxidase
type: Class
subclass of: enzyme label
OBO foundry unique label: visualization of glucose oxidase conjugated to probe
has_obo_namespace: image
id: FBbi:00000178

secondary antibody-glucose oxidase, TNBT
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000179
deprecated: true

secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000180
deprecated: true

secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine silver enhanced
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000181
deprecated: true

secondary antibody-horseradish peroxidase, 4-chloro-1-naphthol
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000182
deprecated: true

secondary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000183
deprecated: true

secondary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000184
deprecated: true

secondary antibody-horseradish peroxidase, Vector NovaRed
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000185
deprecated: true

secondary antibody-horseradish peroxidase, Vector SG
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000186
deprecated: true

secondary antibody-horseradish peroxidase, Vector VIP
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000187
deprecated: true

secondary antibody-phosphatase, Naphthol-AS-BI-phosphate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000188
deprecated: true

secondary antibody-fluor conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000189
deprecated: true

secondary antibody-Alexa Fluor conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000190
deprecated: true

aminomethylcoumarin
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of aminomethylcoumarin conjugated to probe
has_obo_namespace: image
has_related_synonym: AMCA
id: FBbi:00000191

Cascade blue
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Cascade blue conjugated to probe
has_obo_namespace: image
id: FBbi:00000192

secondary antibody-cyanine conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: Cy2
id: FBbi:00000193
deprecated: true

secondary antibody-diaminotriazinylaminoflorescein conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: DTAF
id: FBbi:00000194
deprecated: true

secondary antibody-fluorescein isothiocyanate conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: FITC
id: FBbi:00000195
deprecated: true

secondary antibody-indocarbocyanine conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: Cy3
id: FBbi:00000196
deprecated: true

secondary antibody-indodicarbocyanine conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: Cy5
id: FBbi:00000197
deprecated: true

secondary antibody-lissamine rhodamine sulfonyl chloride
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: LSRC
id: FBbi:00000198
deprecated: true

secondary antibody-rhodamine red-X conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: RRX
id: FBbi:00000199
deprecated: true

secondary antibody-tetramethyl rhodamine isothiocyanate conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: TRITC
id: FBbi:00000200
deprecated: true

secondary antibody-Texas red conjugate
type: Class
subclass of: Thing
has_obo_namespace: image
has_related_synonym: TR
id: FBbi:00000201
deprecated: true

gold
type: Class
subclass of: electron dense label
OBO foundry unique label: visualization of gold conjugated to probe
has_obo_namespace: image
id: FBbi:00000202

labeled nucleic acid probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000203
deprecated: true

DNA probe
type: Class
subclass of: sequence-specific nucleic acid probe
OBO foundry unique label: visualization of DNA probe
has_obo_namespace: image
id: FBbi:00000204

biotin labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000205
deprecated: true

digoxigenin labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000206
deprecated: true

fluor labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000207
deprecated: true

BODIPY TR-14-dUTP labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000208
deprecated: true

bromodeoxyuridine labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000209
deprecated: true

fluoresceine-12-dUTP labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000210
deprecated: true

Oregon Green 488-5-dUTP labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000211
deprecated: true

radioisotope labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000212
deprecated: true

[32]P labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000213
deprecated: true

[33]P labeled DNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000214
deprecated: true

RNA probe
type: Class
subclass of: sequence-specific nucleic acid probe
OBO foundry unique label: visualization of RNA probe
has_obo_namespace: image
id: FBbi:00000215

biotin labeled RNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000216
deprecated: true

digoxigenin labeled RNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000217
deprecated: true

fluoroscein labeled RNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000218
deprecated: true

radioisotope labeled RNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000219
deprecated: true

[32]P labeled RNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000220
deprecated: true

[33]P labeled RNA probe
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000221
deprecated: true

imaging method
type: Class
subclass of: method involved in biological imaging
has_obo_namespace: image
id: FBbi:00000222

graphic illustration
type: Class
subclass of: portrayed image
has_obo_namespace: image
id: FBbi:00000223

computer graphic
type: Class
subclass of: graphic illustration
has_obo_namespace: image
id: FBbi:00000224

black and white graphic
type: Class
subclass of: computer graphic
has_obo_namespace: image
id: FBbi:00000225

color graphic
type: Class
subclass of: computer graphic
has_obo_namespace: image
id: FBbi:00000226

grey scale graphic
type: Class
subclass of: computer graphic
has_obo_namespace: image
id: FBbi:00000227

camera lucida assisted graphic
type: Class
subclass of: graphic illustration
has_obo_namespace: image
id: FBbi:00000228

free hand graphic
type: Class
subclass of: graphic illustration
has_obo_namespace: image
id: FBbi:00000229

line art graphic
type: Class
subclass of: graphic illustration
has_obo_namespace: image
id: FBbi:00000230

charcoal pencil graphic
type: Class
subclass of: line art graphic
has_obo_namespace: image
id: FBbi:00000231

colored pencil graphic
type: Class
subclass of: line art graphic
has_obo_namespace: image
id: FBbi:00000232

graphite pencil graphic
type: Class
subclass of: line art graphic
has_obo_namespace: image
id: FBbi:00000233

pen and ink graphic
type: Class
subclass of: line art graphic
has_obo_namespace: image
has_related_synonym: black and white graphic
id: FBbi:00000234

painted graphic
type: Class
subclass of: line art graphic
has_obo_namespace: image
id: FBbi:00000235

acrylic painted graphic
type: Class
subclass of: painted graphic
has_obo_namespace: image
id: FBbi:00000236

oil painted graphic
type: Class
subclass of: painted graphic
has_obo_namespace: image
id: FBbi:00000237

pastel painted graphic
type: Class
subclass of: painted graphic
has_obo_namespace: image
id: FBbi:00000238

watercolor painted graphic
type: Class
subclass of: painted graphic
has_obo_namespace: image
id: FBbi:00000239

macroscopy
type: Class
subclass of: recorded image
definition: methods for imaging objects large enough to be observed by the unaided eye
has_obo_namespace: image
id: FBbi:00000240
in_subset: PhenoImageShare ImagingMethod

microscopy
type: Class
subclass of: recorded image
definition: methods for forming images of objects too small to be observed with the unaided eye
has_obo_namespace: image
id: FBbi:00000241
in_subset: PhenoImageShare ImagingMethod

wide field light micrograph
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000242
deprecated: true

bright-field microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: widefield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: wide-field detection
  intersection of: Restriction
    on property: makes_use_of
    some values from: absorption of illumination
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: widefield illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: wide-field detection
subclass of: Restriction
  on property: makes_use_of
  some values from: absorption of illumination
has_obo_namespace: image
id: FBbi:00000243
in_subset: PhenoImageShare ImagingMethod

dark-field microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: darkfield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: elastic scattering
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: darkfield illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: elastic scattering
definition: imaging with rejection of the unscattered illumination (removal of the zero order component of the diffracted wave)
has_obo_namespace: image
id: FBbi:00000244
in_subset: PhenoImageShare ImagingMethod

differential interference contrast microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: optical path length gradient
  intersection of: Restriction
    on property: makes_use_of
    some values from: Wollaston prism
  intersection of: Restriction
    on property: makes_use_of
    some values from: polarized light illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: polarization-sensitive detection
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: optical path length gradient
subclass of: Restriction
  on property: makes_use_of
  some values from: Wollaston prism
subclass of: Restriction
  on property: makes_use_of
  some values from: polarized light illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: polarization-sensitive detection
has_obo_namespace: image
has_related_synonym: DIC
has_related_synonym: Nomarski
id: FBbi:00000245

fluorescence microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: fluorescence emission
  intersection of: Restriction
    on property: makes_use_of
    some values from: UV/visible/IR illumination
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: fluorescence emission
has_obo_namespace: image
id: FBbi:00000246
in_subset: PhenoImageShare ImagingMethod

phase contrast microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: hollow-cone illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: refractive index
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: hollow-cone illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: refractive index
has_obo_namespace: image
id: FBbi:00000247

polarization microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: retardance
  intersection of: Restriction
    on property: makes_use_of
    some values from: polarized light illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: polarization-sensitive detection
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: retardance
subclass of: Restriction
  on property: makes_use_of
  some values from: polarized light illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: polarization-sensitive detection
has_obo_namespace: image
id: FBbi:00000248

time lapse microscopy
type: Class
subclass of: light microscopy
has_obo_namespace: image
id: FBbi:00000249

narrow field light micrograph
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi:00000250
deprecated: true

confocal microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrowfield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrow-field detection
  intersection of: Restriction
    on property: makes_use_of
    some values from: fluorescence emission
subclass of: fluorescence microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: narrowfield illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: narrow-field detection
has_obo_namespace: image
id: FBbi:00000251
in_subset: PhenoImageShare ImagingMethod

single-spot confocal microscopy
type: Class
equivalent class: Class
  intersection of: confocal microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: single point scanning
  intersection of: Restriction
    on property: makes_use_of
    some values from: spot detector
subclass of: confocal microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: single point scanning
subclass of: Restriction
  on property: makes_use_of
  some values from: spot detector
has_obo_namespace: image
id: FBbi:00000252

spinning disk confocal microscopy
type: Class
equivalent class: Class
  intersection of: confocal microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: spinning disk scanning
  intersection of: Restriction
    on property: makes_use_of
    some values from: charge coupled device (CCD)
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrow-field detection
subclass of: confocal microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: spinning disk scanning
subclass of: Restriction
  on property: makes_use_of
  some values from: charge coupled device (CCD)
has_obo_namespace: image
id: FBbi:00000253

two-photon laser scanning microscopy
type: Class
subclass of: multi-photon microscopy
has_obo_namespace: image
id: FBbi:00000254

multi-photon microscopy
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrowfield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: pulsed illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: fluorescence emission
subclass of: fluorescence microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: narrowfield illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: pulsed illumination
has_obo_namespace: image
id: FBbi:00000255

electron microscopy
type: Class
equivalent class: Class
  intersection of: microscopy with lenses
  intersection of: Restriction
    on property: makes_use_of
    some values from: illumination by electrons
subclass of: microscopy with lenses
subclass of: Restriction
  on property: makes_use_of
  some values from: illumination by electrons
has_obo_namespace: image
has_related_synonym: mode of electron microscopy
id: FBbi:00000256
in_subset: PhenoImageShare ImagingMethod

scanning electron microscopy (SEM)
type: Class
equivalent class: Class
  intersection of: electron microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrowfield illumination
subclass of: electron microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: narrowfield illumination
definition: image is formed by scanning the surface of the specimen with a beam of electrons in a raster pattern
has_obo_namespace: image
id: FBbi:00000257
in_subset: PhenoImageShare ImagingMethod

transmission electron microscopy (TEM)
type: Class
equivalent class: Class
  intersection of: electron microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: widefield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: wide-field detection
subclass of: electron microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: widefield illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: wide-field detection
has_obo_namespace: image
id: FBbi:00000258

atomic force microscopy
type: Class
subclass of: scanning probe microscopy
definition: the scanning probe is maintained at a fixed distance above the surface e of the specimen by van der Waals forces
has_obo_namespace: image
id: FBbi:00000259

X-ray microscopy
type: Class
equivalent class: Class
  intersection of: microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: X-ray illumination
subclass of: microscopy
subclass of: X-ray radiography
database_cross_reference: http://en.wikipedia.org/wiki/X-ray_microscope
has_obo_namespace: image
id: FBbi:00000260

montage
type: Class
subclass of: portrayed image
has_obo_namespace: image
id: FBbi:00000261

detergent permeabilized
type: Class
subclass of: permeabilized tissue
definition: Membrane permeabilization by the action of ionic or non-ionic detergents
created by: jm
creation date: 2010-03-07T02:37:21Z
has_obo_namespace: image
id: FBbi:00000262

solvent permeabilized
type: Class
subclass of: permeabilized tissue
definition: permeabilization due to extraction of lipid from membranes by an organic solvent such as acetone or methanol.
created by: jm
creation date: 2010-03-07T02:37:29Z
has_obo_namespace: image
id: FBbi:00000263

saponin permeabilized
type: Class
subclass of: permeabilized tissue
definition: Saponin, a detergent-like molecule, preferentially forms holes in membranes that contain cholesterol.
created by: jm
creation date: 2010-03-07T02:43:41Z
has_obo_namespace: image
has_related_synonym: saponized tissue
id: FBbi:00000264

recorded image
type: Class
subclass of: imaging method
definition: methods and devices used for capturing an image of a real object; distinct from images created by artwork
OBO foundry unique label: image recording method
created by: jm
creation date: 2010-03-09T09:57:38Z
has_obo_namespace: image
has_related_synonym: photograph
id: FBbi:00000265

portrayed image
type: Class
subclass of: imaging method
definition: methods and devices used for creating images by some form of artwork, as distinct from capturing images by means of some recording device
OBO foundry unique label: image portrayal method
created by: jm
creation date: 2010-03-09T10:04:40Z
has_obo_namespace: image
has_related_synonym: artwork
has_related_synonym: drawing
id: FBbi:00000266

animation
type: Class
subclass of: computer graphic
definition: A form of graphical illustration that changes with time to give a sense of motion or represent dynamic changes in the portrayal.
created by: jm
creation date: 2010-03-09T10:12:11Z
has_obo_namespace: image
id: FBbi:00000267

illumination method
type: Class
subclass of: method involved in biological imaging
definition: sources and methods for illumination
created by: jm
creation date: 2010-03-09T10:38:14Z
has_obo_namespace: image
id: FBbi:00000268

detection method
type: Class
subclass of: method involved in biological imaging
definition: media and devices employed for recording the alterations in the illumination that result from its interaction with the sample
created by: jm
creation date: 2010-03-09T10:38:14Z
has_obo_namespace: image
id: FBbi:00000269

imaged parameter
type: Class
subclass of: method involved in biological imaging
definition: The physical property of the specimen that leads to the modifications of the illumination that are recorded in the image.
created by: jm
creation date: 2010-03-09T10:38:14Z
has_obo_namespace: image
id: FBbi:00000270

contrast-enhancing method
type: Class
subclass of: method involved in biological imaging
created by: jm
creation date: 2010-03-09T10:38:14Z
has_obo_namespace: image
id: FBbi:00000271

illumination by photons
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:46:27Z
has_obo_namespace: image
id: FBbi:00000272

illumination by electrons
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:46:27Z
has_obo_namespace: image
id: FBbi:00000273

illumination by acoustic waves
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:46:27Z
has_obo_namespace: image
id: FBbi:00000274

illumination by neutrons
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:46:27Z
has_obo_namespace: image
id: FBbi:00000275

illumination by ions
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:46:27Z
has_obo_namespace: image
id: FBbi:00000276

widefield illumination
type: Class
subclass of: illumination method
definition: illumination that covers the entire field of view of the image-forming lens
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000277

narrowfield illumination
type: Class
subclass of: illumination method
definition: illumination restricted to a small portion of the field of view of the imaging lens; often one or more diffraction limited spots
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000278

coherent illumination
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000279

incoherent illumination
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000280

nearfield illumination
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000281

farfield illumination
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000282

continuous illumination
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000283

pulsed illumination
type: Class
subclass of: illumination method
definition: illumination that varies with time; often achieved with pulsed lasers for the purpose of generating very-high peak illumination power
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000284

oblique illumination
type: Class
subclass of: illumination method
created by: jm
creation date: 2010-03-09T10:50:41Z
has_obo_namespace: image
id: FBbi:00000285

single point scanning
type: Class
subclass of: narrowfield illumination
definition: illumination by a single spot of light that is scanned across the field of view
created by: jm
creation date: 2010-03-09T10:51:29Z
has_obo_namespace: image
id: FBbi:00000286

multiple point scanning
type: Class
subclass of: narrowfield illumination
definition: illumination by multiple points of light simultaneously
created by: jm
creation date: 2010-03-09T10:51:29Z
has_obo_namespace: image
id: FBbi:00000287

spinning disk scanning
type: Class
subclass of: multiple point scanning
definition: scanning by multiple points of light arising from pinholes in a spinning disk that is illuminated by a widefield source
created by: jm
creation date: 2010-03-09T10:52:38Z
has_obo_namespace: image
id: FBbi:00000288

array scanning
type: Class
subclass of: multiple point scanning
definition: Multiple points of illumination generated by a fixed array of sources.
created by: jm
creation date: 2010-03-09T10:52:38Z
has_obo_namespace: image
id: FBbi:00000289

hollow-cone illumination
type: Class
subclass of: oblique illumination
definition: illumination parallel or at small angles to the optical axis is attenuated or blocked by a stop
created by: jm
creation date: 2010-03-09T11:04:14Z
has_obo_namespace: image
id: FBbi:00000290

anaxial illumination
type: Class
subclass of: oblique illumination
definition: Illumination is distributed asymmetrically around the optic axis, typically achieved by a non-circular stop placed below the lower lens element and aperture of the condenser.
created by: jm
creation date: 2010-03-09T11:04:14Z
has_obo_namespace: image
id: FBbi:00000291

Axiom
annotated source: anaxial illumination
annotated property: definition
annotated target: Illumination is distributed asymmetrically around the optic axis, typically achieved by a non-circular stop placed below the lower lens element and aperture of the condenser.
database_cross_reference: :

darkfield illumination
type: Class
subclass of: hollow-cone illumination
definition: illumination restricted to angles that exceed the acceptance angle of the image-forming lens
created by: jm
creation date: 2010-03-09T11:04:41Z
has_obo_namespace: image
id: FBbi:00000292

Rheinberg illumination
type: Class
subclass of: hollow-cone illumination
definition: illumination at angles less than the acceptance angle of the image-forming lens is attenuated by a filter to give a colored background of unscattered light; higher angle illumination may be filtered to give a contrasting color
created by: jm
creation date: 2010-03-09T11:04:41Z
has_obo_namespace: image
id: FBbi:00000293

charge coupled device (CCD)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000294

photomultiplier tube (PMT)
type: Class
subclass of: spot detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000295

photodiode
type: Class
subclass of: spot detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000296

avalanche photodiode (APD)
type: Class
subclass of: spot detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000297

silicon intensified target tube (SIT)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000298

intensified SIT (ISIT)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000299

intensified CCD (ICCD)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000300

electron multiplying CCD (EMCCD)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000301

electron bombardment CCD (EBCCD)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000302

film
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000303

complementary metal oxide semiconductor (CMOS)
type: Class
subclass of: area detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000304

piezo-electric device
type: Class
subclass of: spot detector
created by: jm
creation date: 2010-03-09T11:33:49Z
has_obo_namespace: image
id: FBbi:00000305

wide-field detection
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-09T12:45:35Z
has_obo_namespace: image
id: FBbi:00000306

narrow-field detection
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-09T12:45:35Z
has_obo_namespace: image
id: FBbi:00000307

absorption of illumination
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000308

inelastic scattering
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000309

elastic scattering
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000310

refractive index
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000311

optical path length gradient
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000312

retardance
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000313

stiffness
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000314

electron density
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000315

fluorescence emission
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000316

sub-nanosecond time-resolved fluorescence emission)
type: Class
subclass of: fluorescence emission
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000317

fluorescence polarization (polarization angle resolved fluorescence emission)
type: Class
subclass of: fluorescence emission
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000318

chemical composition
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000319

elevation
type: Class
subclass of: imaged parameter
created by: jm
creation date: 2010-03-09T03:11:47Z
has_obo_namespace: image
id: FBbi:00000320

resolution-enhancing method
type: Class
subclass of: method involved in biological imaging
definition: methods for increasing the resolution beyond the classical Abbe diffraction limit
created by: jm
creation date: 2010-03-09T03:12:34Z
has_obo_namespace: image
id: FBbi:00000321

optical method
type: Class
subclass of: contrast-enhancing method
OBO foundry unique label: optical contrast enhancing method
created by: jm
creation date: 2010-03-09T03:14:53Z
has_obo_namespace: image
id: FBbi:00000322

computational method
type: Class
subclass of: contrast-enhancing method
OBO foundry unique label: computational contrast enhancing method
created by: jm
creation date: 2010-03-09T03:14:53Z
has_obo_namespace: image
id: FBbi:00000323

in-focus phase contrast
type: Class
subclass of: modified objective lens
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000324

defocus phase contrast
type: Class
subclass of: optical method
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000325

Wollaston prism
type: Class
subclass of: optical method
definition: a birefringent optical element typically used to split polarized illumination into two sets of parallel but displaced rays
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000326

Hoffman modulation
type: Class
subclass of: modified objective lens
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000327

single sideband edge enhancement (SSBE)
type: Class
subclass of: modified objective lens
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000328

interference reflection contrast (IRM)
type: Class
subclass of: optical method
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000329

interference contrast
type: Class
subclass of: optical method
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000330

polarization contrast
type: Class
subclass of: optical method
created by: jm
creation date: 2010-03-09T03:20:14Z
has_obo_namespace: image
id: FBbi:00000331

structured illumination microscopy (SIM)
type: Class
subclass of: resolution-enhancing method
created by: jm
creation date: 2010-03-09T03:24:02Z
has_obo_namespace: image
id: FBbi:00000332

point-localization method
type: Class
subclass of: resolution-enhancing method
created by: jm
creation date: 2010-03-09T03:24:02Z
has_obo_namespace: image
id: FBbi:00000333

stimulated emission depletion (STED)
type: Class
equivalent class: Class
  intersection of: resolution-enhancing method
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrowfield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: emission-depletion illumination
subclass of: resolution-enhancing method
subclass of: Restriction
  on property: makes_use_of
  some values from: narrowfield illumination
subclass of: Restriction
  on property: makes_use_of
  some values from: emission-depletion illumination
created by: jm
creation date: 2010-03-09T03:24:02Z
has_obo_namespace: image
id: FBbi:00000334

PALM (photoactivation localization microscopy)
type: Class
equivalent class: Class
  intersection of: point-localization method
  intersection of: Restriction
    on property: makes_use_of
    some values from: photo-activation illumination
subclass of: point-localization method
subclass of: Restriction
  on property: makes_use_of
  some values from: photo-activation illumination
created by: jm
creation date: 2010-03-09T03:32:12Z
has_obo_namespace: image
id: FBbi:00000335

STORM (stochastic optical reconstruction microscopy)
type: Class
equivalent class: Class
  intersection of: point-localization method
  intersection of: Restriction
    on property: makes_use_of
    some values from: photo-switching illumination
subclass of: point-localization method
subclass of: Restriction
  on property: makes_use_of
  some values from: photo-switching illumination
created by: jm
creation date: 2010-03-09T03:32:12Z
has_obo_namespace: image
id: FBbi:00000336

FIONA (fluorescence imaging with one nanometer accuracy)
type: Class
subclass of: point-localization method
created by: jm
creation date: 2010-03-09T03:32:12Z
has_obo_namespace: image
id: FBbi:00000337

DOPI (defocussed orientation and position imaging)
type: Class
subclass of: point-localization method
created by: jm
creation date: 2010-03-09T03:32:12Z
has_obo_namespace: image
id: FBbi:00000338

PAINT (point accumulation for imaging in nanoscale topography)
type: Class
subclass of: point-localization method
created by: jm
creation date: 2010-03-09T03:32:12Z
has_obo_namespace: image
id: FBbi:00000339

saturated structured-illumination microscopy (SSIM)
type: Class
subclass of: structured illumination microscopy (SIM)
definition: structured illumination used at sufficiently high power to cause significant ground-state depletion of the imaged fluorophore, thus allowing for non-linear resolution enhancement
created by: jm
creation date: 2010-03-09T03:32:29Z
has_obo_namespace: image
id: FBbi:00000340

UV/visible/IR illumination
type: Class
subclass of: illumination by photons
created by: jm
creation date: 2010-03-09T03:51:49Z
has_obo_namespace: image
id: FBbi:00000341

X-ray illumination
type: Class
subclass of: x-ray/gamma ray illumination
created by: jm
creation date: 2010-03-09T03:51:49Z
has_obo_namespace: image
id: FBbi:00000342

microscopy with lenses
type: Class
subclass of: microscopy
created by: jm
creation date: 2010-03-09T04:04:04Z
has_obo_namespace: image
id: FBbi:00000343

scanning probe microscopy
type: Class
subclass of: microscopy
definition: imaging by means of a physical probe that passes over the sample
created by: jm
creation date: 2010-03-09T04:04:04Z
has_obo_namespace: image
id: FBbi:00000344

light microscopy
type: Class
equivalent class: Class
  intersection of: microscopy with lenses
  intersection of: Restriction
    on property: makes_use_of
    some values from: UV/visible/IR illumination
subclass of: microscopy with lenses
subclass of: Restriction
  on property: makes_use_of
  some values from: UV/visible/IR illumination
created by: jm
creation date: 2010-03-09T04:18:03Z
has_obo_namespace: image
has_related_synonym: mode of light microscopy
id: FBbi:00000345
in_subset: PhenoImageShare ImagingMethod

scanning tunneling microscopy
type: Class
subclass of: scanning probe microscopy
created by: jm
creation date: 2010-03-09T10:19:35Z
has_obo_namespace: image
id: FBbi:00000347

nearfield scanning optical microscopy (ANSOM)
type: Class
subclass of: scanning probe microscopy
created by: jm
creation date: 2010-03-09T10:19:35Z
has_obo_namespace: image
id: FBbi:00000348

ANSOM
type: Class
subclass of: nearfield scanning optical microscopy (ANSOM)
definition: Aperture-less NSOM.
created by: jm
creation date: 2010-03-09T10:20:01Z
has_obo_namespace: image
id: FBbi:00000349

polarized light illumination
type: Class
subclass of: illumination by photons
created by: jm
creation date: 2010-03-09T10:23:41Z
has_obo_namespace: image
id: FBbi:00000350

orientation-independent polarization microscopy
type: Class
subclass of: polarization microscopy
created by: jm
creation date: 2010-03-09T10:25:08Z
has_obo_namespace: image
id: FBbi:00000351

polarization-sensitive detection
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-09T10:27:11Z
has_obo_namespace: image
id: FBbi:00000352

modified objective lens
type: Class
subclass of: optical method
definition: Uses an objective with extra components to manipulate the wave front in the plane of the objective aperture.
created by: jm
creation date: 2010-03-09T10:41:27Z
has_obo_namespace: image
id: FBbi:00000353

linear method
type: Class
subclass of: computational method
disjoint with: non-linear method
definition: a computational method that is linear in the mathematical sense, meaning that image intensity is conserved and the data remain suitable for all quantitative analyses
OBO foundry unique label: linear computational contrast enhancing method method
created by: jm
creation date: 2010-03-09T11:09:35Z
has_obo_namespace: image
id: FBbi:00000354

non-linear method
type: Class
subclass of: computational method
definition: computational method that are mathematically non-linear; image intensity is not conserved, and the data are in general not suitable for quantitative analyses of pixel values
OBO foundry unique label: non-linear computational contrast enhancing method method
created by: jm
creation date: 2010-03-09T11:09:35Z
has_obo_namespace: image
id: FBbi:00000355

Wiener filter
type: Class
subclass of: linear method
created by: jm
creation date: 2010-03-09T11:10:59Z
has_obo_namespace: image
id: FBbi:00000356

3D-deconvolution
type: Class
subclass of: linear method
created by: jm
creation date: 2010-03-09T11:10:59Z
has_obo_namespace: image
id: FBbi:00000357

no-neighbors deblurring
type: Class
subclass of: non-linear method
created by: jm
creation date: 2010-03-09T11:11:56Z
has_obo_namespace: image
id: FBbi:00000358

nearest-neighbors deblurring
type: Class
subclass of: non-linear method
created by: jm
creation date: 2010-03-09T11:11:56Z
has_obo_namespace: image
id: FBbi:00000359

constrained iterative deconvolution
type: Class
subclass of: 3D-deconvolution
created by: jm
creation date: 2010-03-09T11:19:41Z
has_obo_namespace: image
id: FBbi:00000360

maximum likelihood deconvolution
type: Class
subclass of: 3D-deconvolution
created by: jm
creation date: 2010-03-09T11:19:41Z
has_obo_namespace: image
id: FBbi:00000361

blind deconvolution
type: Class
subclass of: 3D-deconvolution
created by: jm
creation date: 2010-03-09T11:19:41Z
has_obo_namespace: image
id: FBbi:00000362

exhaustive photon reassignment
type: Class
subclass of: 3D-deconvolution
created by: jm
creation date: 2010-03-09T11:19:42Z
has_obo_namespace: image
id: FBbi:00000363

light-sheet illumination
type: Class
subclass of: oblique illumination
definition: illumination in the form of a thin sheet of light directed perpendicular to the optic axis
created by: jm
creation date: 2010-03-11T10:06:20Z
has_obo_namespace: image
id: FBbi:00000364

FLIP
type: Class
equivalent class: Class
  intersection of: fluorescence microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: photo-bleaching illumination
subclass of: fluorescence microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: photo-bleaching illumination
definition: Fluorescence loss in photobleaching; a method of determining whether two populations of fluorophore are in diffusive communication with one another by observing the decrease in brightness of one population when the other population is subjected to continuous photobleaching.
created by: jm
creation date: 2010-03-11T10:09:33Z
has_obo_namespace: image
id: FBbi:00000365

FRAP
type: Class
equivalent class: Class
  intersection of: fluorescence microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: narrowfield illumination
  intersection of: Restriction
    on property: makes_use_of
    some values from: photo-bleaching illumination
subclass of: FLIP
subclass of: Restriction
  on property: makes_use_of
  some values from: narrowfield illumination
definition: Fluorescence loss in photobleaching; a method of determining the rate and extent of exchange between a localized population of fluorophore and a non-localized diffusible pool, by observing the rate of recovery of brightness of the localized population after photobleaching.
created by: jm
creation date: 2010-03-11T10:09:33Z
has_obo_namespace: image
id: FBbi:00000366

Axiom
annotated source: FRAP
annotated property: definition
annotated target: Fluorescence loss in photobleaching; a method of determining the rate and extent of exchange between a localized population of fluorophore and a non-localized diffusible pool, by observing the rate of recovery of brightness of the localized population after photobleaching.
database_cross_reference: XX:-new-dbxref-

FRET
type: Class
subclass of: fluorescence microscopy
definition: Fluorescence (or Forster) resonance energy transfer; a method of estimating the distance between two fluorophores by measuring the extent of non-radiative energy transfer between the two. Experimentally, this involves selective excitation of one while observing emission from the other.
created by: jm
creation date: 2010-03-11T10:09:33Z
has_obo_namespace: image
id: FBbi:00000367

FLIM
type: Class
subclass of: fluorescence microscopy
created by: jm
creation date: 2010-03-11T10:09:33Z
has_obo_namespace: image
id: FBbi:00000368

SPIM
type: Class
equivalent class: Class
  intersection of: fluorescence microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: light-sheet illumination
subclass of: fluorescence microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: light-sheet illumination
definition: single (or selective) plane illumination.
created by: jm
creation date: 2010-03-11T10:09:33Z
has_obo_namespace: image
id: FBbi:00000369

CARS
type: Class
equivalent class: Class
  intersection of: light microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: inelastic scattering
  intersection of: Restriction
    on property: makes_use_of
    some values from: chemical composition
subclass of: light microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: inelastic scattering
subclass of: Restriction
  on property: makes_use_of
  some values from: chemical composition
definition: coherent Raman anti-Stokes microscopy
created by: jm
creation date: 2010-03-11T10:13:20Z
has_obo_namespace: image
id: FBbi:00000370

OCT
type: Class
subclass of: light microscopy
definition: optical coherence tomography; an interferometric method of imaging using back-scattered photons (elastic scattering)
created by: jm
creation date: 2010-03-11T10:32:19Z
has_obo_namespace: image
id: FBbi:00000371

secondary_electron imaging
type: Class
subclass of: scanning electron microscopy (SEM)
definition: image created using the electrons generated by ionization of a sample due to inelastic scattering of the primary beam of radiation
created by: jm
creation date: 2010-03-12T08:34:44Z
has_obo_namespace: image
id: FBbi:00000372

back-scattered_electron imaging
type: Class
subclass of: scanning electron microscopy (SEM)
definition: imaged formed using electrons undergoing elastic scattering at very high angles, with emission of characteristic X-rays
created by: jm
creation date: 2010-03-12T08:40:37Z
has_obo_namespace: image
id: FBbi:00000373

detection of photons
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-12T08:54:56Z
has_obo_namespace: image
id: FBbi:00000374

detection of electrons
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-12T08:54:56Z
has_obo_namespace: image
id: FBbi:00000375

detection of acoustic waves
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-12T08:54:56Z
has_obo_namespace: image
id: FBbi:00000376

detection of current induced in the specimen
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-12T08:54:56Z
has_obo_namespace: image
id: FBbi:00000377

detection of UV/visible/IR photons
type: Class
subclass of: detection of photons
created by: jm
creation date: 2010-03-12T08:55:29Z
has_obo_namespace: image
id: FBbi:00000378

detection of X-ray photons
type: Class
subclass of: detection of photons
created by: jm
creation date: 2010-03-12T08:55:29Z
has_obo_namespace: image
id: FBbi:00000379

scanning-transmission electron microscopy
type: Class
subclass of: electron microscopy
created by: jm
creation date: 2010-03-12T09:12:36Z
has_obo_namespace: image
id: FBbi:00000380

EELS imaging
type: Class
subclass of: electron microscopy
created by: jm
creation date: 2010-03-12T09:16:40Z
has_obo_namespace: image
has_related_synonym: EFTEM energy filtered TEM
has_related_synonym: ESI electron spectroscopic imaging
id: FBbi:00000381

EDAX imaging
type: Class
subclass of: electron microscopy
created by: jm
creation date: 2010-03-12T09:16:40Z
has_obo_namespace: image
id: FBbi:00000382

specimen_modifying_illumination
type: Class
subclass of: illumination method
definition: Illumination used for the purpose of inducing some observable change in the specimen during the course of an imaging session. This illumination may or may not be the same as the illumination used for imaging. Typically used in conjunction with live-cell imaging
created by: jm
creation date: 2010-03-12T09:32:53Z
has_obo_namespace: image
id: FBbi:00000383

photo-bleaching illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000384

photo-ablation illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000385

photo-switching illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000386

photo-activation illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000387

uncaging illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000388

trapping illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000389

emission-depletion illumination
type: Class
subclass of: specimen_modifying_illumination
created by: jm
creation date: 2010-03-12T10:06:46Z
has_obo_namespace: image
id: FBbi:00000390

slit-scanning illumination
type: Class
subclass of: narrowfield illumination
definition: illumination in the shape of a thin line that is swept over the field of view
created by: jm
creation date: 2010-03-12T10:31:26Z
has_obo_namespace: image
id: FBbi:00000391

slit-scan confocal microscopy
type: Class
equivalent class: Class
  intersection of: confocal microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: slit-scanning illumination
subclass of: confocal microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: slit-scanning illumination
definition: illumination and detection via a thin slit
created by: jm
creation date: 2010-03-12T10:32:36Z
has_obo_namespace: image
id: FBbi:00000392

array-scan confocal microscopy
type: Class
equivalent class: Class
  intersection of: confocal microscopy
  intersection of: Restriction
    on property: makes_use_of
    some values from: array scanning
  intersection of: Restriction
    on property: makes_use_of
    some values from: charge coupled device (CCD)
subclass of: confocal microscopy
subclass of: Restriction
  on property: makes_use_of
  some values from: array scanning
subclass of: Restriction
  on property: makes_use_of
  some values from: charge coupled device (CCD)
definition: Fixed array of sources focused to an array of spots that is swept over the specimen in raster fashion
created by: jm
creation date: 2010-03-12T10:35:43Z
has_obo_namespace: image
id: FBbi:00000393

spot detector
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-12T10:39:24Z
has_obo_namespace: image
id: FBbi:00000394

area detector
type: Class
subclass of: detection method
created by: jm
creation date: 2010-03-12T10:39:24Z
has_obo_namespace: image
id: FBbi:00000395

visualization of contiguous regions
type: Class
subclass of: visualization method
definition: methods of visualization that differentiate between different regions or surfaces of the specimen based on contiguity
created by: jm
creation date: 2010-03-14T08:38:50Z
has_obo_namespace: image
id: FBbi:00000396

visualization by chemical attribute
type: Class
subclass of: visualization method
definition: methods of visualization that differentiate regions of the specimen on the basis of their chemical properties
created by: jm
creation date: 2010-03-14T08:38:50Z
has_obo_namespace: image
id: FBbi:00000397

shadowing and plating
type: Class
subclass of: visualization of contiguous regions
subclass of: Restriction
  on property: makes_use_of
  some values from: freeze_fracture/freeze_etch
definition: visualization by depositing a label on the surface of a specimen uniformly (plating), or from a particular direction so that surface topography becomes visible (shadowing)
created by: jm
creation date: 2010-03-14T08:44:06Z
has_obo_namespace: image
id: FBbi:00000398

negative staining
type: Class
subclass of: visualization of contiguous regions
definition: visualization by exclusion of a stain in which the specimen is immersed; compare with "positive staining.
created by: jm
creation date: 2010-03-14T08:44:06Z
has_obo_namespace: image
id: FBbi:00000399

sequence-specific nucleic acid probe
type: Class
subclass of: macromolecular probe
OBO foundry unique label: visualization of sequence-specific nucleic acid probe
created by: jm
creation date: 2010-03-14T09:07:35Z
has_obo_namespace: image
id: FBbi:00000400

antibody
type: Class
subclass of: macromolecular probe
OBO foundry unique label: visualization of antibody
created by: jm
creation date: 2010-03-14T09:07:35Z
has_obo_namespace: image
id: FBbi:00000401

lectin
type: Class
subclass of: macromolecular probe
OBO foundry unique label: visualization of lectin
created by: jm
creation date: 2010-03-14T09:07:35Z
has_obo_namespace: image
id: FBbi:00000402

small-molecule probe
type: Class
subclass of: visualization by chemical attribute
OBO foundry unique label: visualization of small-molecule probe
created by: jm
creation date: 2010-03-14T09:07:35Z
has_obo_namespace: image
id: FBbi:00000403

fluorescent dextran fill
type: Class
subclass of: intracellular filling
created by: jm
creation date: 2010-03-14T10:42:36Z
has_obo_namespace: image
id: FBbi:00000404

fluorescent protein tag
type: Class
subclass of: genetically encoded tag
OBO foundry unique label: visualization of fluorescent protein tag
created by: jm
creation date: 2010-03-14T10:54:20Z
has_obo_namespace: image
id: FBbi:00000405

probes for nucleic acid
type: Class
subclass of: small-molecule probe
OBO foundry unique label: visualization of probes for nucleic acid
created by: jm
creation date: 2010-03-14T09:25:57Z
has_obo_namespace: image
id: FBbi:00000406

small genetically encoded tag
type: Class
subclass of: genetically encoded tag
OBO foundry unique label: visualization of small genetically encoded tag
created by: jm
creation date: 2010-03-14T11:10:25Z
has_obo_namespace: image
id: FBbi:00000407

probe for protein
type: Class
subclass of: small-molecule probe
OBO foundry unique label: visualization of probe for protein
created by: jm
creation date: 2010-03-14T09:25:57Z
has_obo_namespace: image
id: FBbi:00000408

organelle-specific probe
type: Class
subclass of: small-molecule probe
OBO foundry unique label: visualization of organelle-specific probe
created by: jm
creation date: 2010-03-14T09:25:57Z
has_obo_namespace: image
id: FBbi:00000409

macromolecular probe
type: Class
subclass of: visualization by chemical attribute
OBO foundry unique label: visualization of macromolecular probe
created by: jm
creation date: 2010-03-14T09:26:11Z
has_obo_namespace: image
id: FBbi:00000410

probe for mitochondria
type: Class
subclass of: organelle-specific probe
OBO foundry unique label: visualization of probe for mitochondria
created by: jm
creation date: 2010-03-14T09:28:19Z
has_obo_namespace: image
id: FBbi:00000411

probe for endoplasmic reticulum
type: Class
subclass of: organelle-specific probe
OBO foundry unique label: visualization of probe for endoplasmic reticulum
created by: jm
creation date: 2010-03-14T09:28:19Z
has_obo_namespace: image
id: FBbi:00000412

probe for Golgi
type: Class
subclass of: organelle-specific probe
OBO foundry unique label: visualization of probe for Golgi
created by: jm
creation date: 2010-03-14T09:28:19Z
has_obo_namespace: image
id: FBbi:00000413

probe for lysosomes
type: Class
subclass of: organelle-specific probe
OBO foundry unique label: visualization of probe for lysosomes
created by: jm
creation date: 2010-03-14T09:28:19Z
has_obo_namespace: image
id: FBbi:00000414

stain with broad specificity
type: Class
subclass of: small-molecule probe
OBO foundry unique label: visualization of stain with broad specificity
created by: jm
creation date: 2010-03-15T11:51:34Z
has_obo_namespace: image
has_related_synonym: positive staining
id: FBbi:00000415

tetracysteine tag
type: Class
subclass of: small genetically encoded tag
OBO foundry unique label: visualization of tetracysteine tag
created by: jm
creation date: 2010-03-14T11:12:03Z
has_obo_namespace: image
id: FBbi:00000416

Hoechst 33258
type: Class
subclass of: membrane-permeant probe
OBO foundry unique label: visualization of Hoechst 33258
created by: jm
creation date: 2010-03-14T09:33:18Z
has_obo_namespace: image
id: FBbi:00000417

genetically encoded biotin tag
type: Class
subclass of: small genetically encoded tag
OBO foundry unique label: visualization of genetically encoded biotin tag
created by: jm
creation date: 2010-03-14T11:12:03Z
has_obo_namespace: image
id: FBbi:00000418

freeze_fracture/freeze_etch
type: Class
subclass of: cryofixed tissue
created by: jm
creation date: 2010-03-17T01:55:02Z
has_obo_namespace: image
id: FBbi:00000419

fluorescent protein derived from Aequorea victoria
type: Class
subclass of: fluorescent protein tag
OBO foundry unique label: visualization of fluorescent protein derived from Aequorea victoria
created by: jm
creation date: 2010-03-17T01:59:59Z
has_obo_namespace: image
id: FBbi:00000420

membrane-permeant probe
type: Class
subclass of: probes for nucleic acid
OBO foundry unique label: visualization of membrane-permeant probe
created by: jm
creation date: 2010-03-14T09:33:53Z
has_obo_namespace: image
id: FBbi:00000421

membrane impermeant probe
type: Class
subclass of: probes for nucleic acid
OBO foundry unique label: visualization of membrane impermeant probe
created by: jm
creation date: 2010-03-14T09:33:53Z
has_obo_namespace: image
id: FBbi:00000422

acridine homodimer
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of acridine homodimer
created by: jm
creation date: 2010-03-14T09:42:34Z
has_obo_namespace: image
id: FBbi:00000423

7-amino-actinomycin D
type: Class
subclass of: membrane impermeant probe
OBO foundry unique label: visualization of 7-amino-actinomycin D
created by: jm
creation date: 2010-03-14T09:42:34Z
has_obo_namespace: image
id: FBbi:00000424

conconavalin A
type: Class
subclass of: lectin
OBO foundry unique label: visualization of conconavalin A
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000425

wheat germ agglutinin
type: Class
subclass of: lectin
OBO foundry unique label: visualization of wheat germ agglutinin
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000426

Phaseolus vulgaris lectin PHA-L)
type: Class
subclass of: lectin
OBO foundry unique label: visualization of Phaseolus vulgaris lectin PHA-L)
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000427

Arachis hypogaea (PNA)
type: Class
subclass of: lectin
OBO foundry unique label: visualization of Arachis hypogaea (PNA)
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000428

Helix pomatia agglutinin
type: Class
subclass of: lectin
OBO foundry unique label: visualization of Helix pomatia agglutinin
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000429

soybean agglutinin
type: Class
subclass of: lectin
OBO foundry unique label: visualization of soybean agglutinin
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000430

cholera toxin B
type: Class
subclass of: lectin
OBO foundry unique label: visualization of cholera toxin B
created by: jm
creation date: 2010-03-14T09:48:57Z
has_obo_namespace: image
id: FBbi:00000431

peptide-nucleic acid probe
type: Class
subclass of: sequence-specific nucleic acid probe
OBO foundry unique label: visualization of peptide-nucleic acid probe
created by: jm
creation date: 2010-03-14T09:52:30Z
has_obo_namespace: image
id: FBbi:00000432

fluorescent protein derived from Anthozoa
type: Class
subclass of: fluorescent protein tag
OBO foundry unique label: visualization of fluorescent protein derived from Anthozoa
created by: jm
creation date: 2010-03-17T01:59:59Z
has_obo_namespace: image
id: FBbi:00000433

optical highlighter
type: Class
subclass of: fluorescent protein tag
OBO foundry unique label: visualization of optical highlighter
created by: jm
creation date: 2010-03-17T01:59:59Z
has_obo_namespace: image
id: FBbi:00000434

Blue fluorescent protein from Aequorea victoria
type: Class
subclass of: fluorescent protein derived from Aequorea victoria
OBO foundry unique label: visualization of Blue fluorescent protein from Aequorea victoria
created by: jm
creation date: 2010-03-17T02:01:22Z
has_obo_namespace: image
id: FBbi:00000435

Cyan fluorescent protein from Aequorea
type: Class
subclass of: fluorescent protein derived from Aequorea victoria
OBO foundry unique label: visualization of Cyan fluorescent protein from Aequorea
created by: jm
creation date: 2010-03-17T02:01:22Z
has_obo_namespace: image
id: FBbi:00000436

Green fluorescent protein from Aequorea
type: Class
subclass of: fluorescent protein derived from Aequorea victoria
OBO foundry unique label: visualization of Green fluorescent protein from Aequorea
created by: jm
creation date: 2010-03-17T02:01:22Z
has_obo_namespace: image
id: FBbi:00000437

DiIC16
type: Class
subclass of: probe for lipid
OBO foundry unique label: visualization of DiIC16
created by: jm
creation date: 2010-03-14T10:15:00Z
has_obo_namespace: image
id: FBbi:00000438

Yellow fluorescent protein from Aequorea
type: Class
subclass of: fluorescent protein derived from Aequorea victoria
OBO foundry unique label: visualization of Yellow fluorescent protein from Aequorea
created by: jm
creation date: 2010-03-17T02:01:22Z
has_obo_namespace: image
id: FBbi:00000439

Alexa Fluor 488
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 488 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000440

Alexa Fluor 546
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 546 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000441

Alexa Fluor 568
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 568 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000442

Alexa Fluor 555
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 555 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000443

Alexa Fluor 594
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 594 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000444

Alexa Fluor 610
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 610 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000445

Alexa Fluor 633
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 633 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000446

Alexa Fluor 647
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Alexa Fluor 647 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000447

Cy2
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Cy2 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000448

Cy3
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Cy3 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000449

Cy5
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Cy5 conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000450

Fluorescein (FITC)
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Fluorescein (FITC) conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000451

Rhodamine
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of Rhodamine conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000452

TexasRed
type: Class
subclass of: fluorescent label
definition: fluorophore with ex/em 589/615
OBO foundry unique label: visualization of TexasRed conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000453

Tetramethyl rhodamine (TRITC)
type: Class
subclass of: fluorescent label
definition: fluorophore derivative of rhodamine with ex/em 547/572
OBO foundry unique label: visualization of Tetramethyl rhodamine (TRITC) conjugated to probe
created by: jm
creation date: 2010-03-14T10:22:41Z
has_obo_namespace: image
id: FBbi:00000454

fluorescent label
type: Class
subclass of: vizualization of label conjugated to probe
OBO foundry unique label: visualization of fluorescent label conjugated to probe
created by: jm
creation date: 2010-03-14T10:25:58Z
has_obo_namespace: image
id: FBbi:00000455

enzyme label
type: Class
subclass of: vizualization of label conjugated to probe
OBO foundry unique label: visualization of enzyme label conjugated to probe
created by: jm
creation date: 2010-03-14T10:25:58Z
has_obo_namespace: image
id: FBbi:00000456

electron dense label
type: Class
subclass of: vizualization of label conjugated to probe
OBO foundry unique label: visualization of electron dense label conjugated to probe
created by: jm
creation date: 2010-03-14T10:25:58Z
has_obo_namespace: image
id: FBbi:00000457

biotin
type: Class
subclass of: fluorescent label
OBO foundry unique label: visualization of biotin conjugated to probe
created by: jm
creation date: 2010-03-14T10:25:58Z
has_obo_namespace: image
id: FBbi:00000458

affinity for specific proteins
type: Class
subclass of: probe for protein
OBO foundry unique label: visualization of affinity for specific proteins
created by: jm
creation date: 2010-03-14T10:28:34Z
has_obo_namespace: image
id: FBbi:00000459

non-specific protein affinity
type: Class
subclass of: probe for protein
OBO foundry unique label: visualization of non-specific protein affinity
created by: jm
creation date: 2010-03-14T10:28:34Z
has_obo_namespace: image
id: FBbi:00000460

AzuriteFP
type: Class
subclass of: Blue fluorescent protein from Aequorea victoria
OBO foundry unique label: visualization of AzuriteFP
created by: jm
creation date: 2010-03-17T02:09:45Z
has_obo_namespace: image
id: FBbi:00000461

SiriusFP
type: Class
subclass of: Blue fluorescent protein from Aequorea victoria
OBO foundry unique label: visualization of SiriusFP
created by: jm
creation date: 2010-03-17T02:09:45Z
has_obo_namespace: image
id: FBbi:00000462

non-immunological protein probe
type: Class
subclass of: macromolecular probe
OBO foundry unique label: visualization of non-immunological protein probe
created by: jm
creation date: 2010-03-14T10:32:01Z
has_obo_namespace: image
id: FBbi:00000463

alpha-bungarotoxin
type: Class
subclass of: non-immunological protein probe
OBO foundry unique label: visualization of alpha-bungarotoxin
created by: jm
creation date: 2010-03-14T10:36:52Z
has_obo_namespace: image
id: FBbi:00000464

botulinum toxin
type: Class
subclass of: non-immunological protein probe
OBO foundry unique label: visualization of botulinum toxin
created by: jm
creation date: 2010-03-14T10:36:52Z
has_obo_namespace: image
id: FBbi:00000465

tetrodotoxin
type: Class
subclass of: affinity for specific proteins
OBO foundry unique label: visualization of tetrodotoxin
created by: jm
creation date: 2010-03-14T10:37:23Z
has_obo_namespace: image
id: FBbi:00000466

batrachatoxin
type: Class
subclass of: affinity for specific proteins
OBO foundry unique label: visualization of batrachatoxin
created by: jm
creation date: 2010-03-14T10:37:23Z
has_obo_namespace: image
id: FBbi:00000467

CeruleanFP
type: Class
subclass of: Cyan fluorescent protein from Aequorea
OBO foundry unique label: visualization of CeruleanFP
created by: jm
creation date: 2010-03-17T02:10:21Z
has_obo_namespace: image
id: FBbi:00000468

CyPet
type: Class
subclass of: Cyan fluorescent protein from Aequorea
OBO foundry unique label: visualization of CyPet
created by: jm
creation date: 2010-03-17T02:10:21Z
has_obo_namespace: image
id: FBbi:00000469

SCFP
type: Class
subclass of: Cyan fluorescent protein from Aequorea
OBO foundry unique label: visualization of SCFP
created by: jm
creation date: 2010-03-17T02:10:21Z
has_obo_namespace: image
id: FBbi:00000470

EmeraldFP
type: Class
subclass of: Green fluorescent protein from Aequorea
OBO foundry unique label: visualization of EmeraldFP
created by: jm
creation date: 2010-03-17T02:11:07Z
has_obo_namespace: image
id: FBbi:00000471

SuperfolderFP
type: Class
subclass of: Green fluorescent protein from Aequorea
OBO foundry unique label: visualization of SuperfolderFP
created by: jm
creation date: 2010-03-17T02:11:07Z
has_obo_namespace: image
id: FBbi:00000472

T-SapphireFP
type: Class
subclass of: Green fluorescent protein from Aequorea
OBO foundry unique label: visualization of T-SapphireFP
created by: jm
creation date: 2010-03-17T02:11:07Z
has_obo_namespace: image
id: FBbi:00000473

CitrineFP
type: Class
subclass of: Yellow fluorescent protein from Aequorea
OBO foundry unique label: visualization of CitrineFP
created by: jm
creation date: 2010-03-17T02:14:30Z
has_obo_namespace: image
id: FBbi:00000474

SYFP
type: Class
subclass of: Yellow fluorescent protein from Aequorea
OBO foundry unique label: visualization of SYFP
created by: jm
creation date: 2010-03-17T02:14:30Z
has_obo_namespace: image
id: FBbi:00000475

TopazFP
type: Class
subclass of: Yellow fluorescent protein from Aequorea
OBO foundry unique label: visualization of TopazFP
created by: jm
creation date: 2010-03-17T02:14:30Z
has_obo_namespace: image
id: FBbi:00000476

VenusFP
type: Class
subclass of: Yellow fluorescent protein from Aequorea
OBO foundry unique label: visualization of VenusFP
created by: jm
creation date: 2010-03-17T02:14:30Z
has_obo_namespace: image
id: FBbi:00000477

yPet
type: Class
subclass of: Yellow fluorescent protein from Aequorea
OBO foundry unique label: visualization of yPet
created by: jm
creation date: 2010-03-17T02:14:30Z
has_obo_namespace: image
id: FBbi:00000478

Blue fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Blue fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000479

Cyan fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Cyan fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000480

Green fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Green fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000481

Orange fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Orange fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000482

Red fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Red fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000483

Far-red fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Far-red fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000484

Yellow fluorescent proteins from Anthozoa
type: Class
subclass of: fluorescent protein derived from Anthozoa
OBO foundry unique label: visualization of Yellow fluorescent proteins from Anthozoa
created by: jm
creation date: 2010-03-17T02:16:24Z
has_obo_namespace: image
id: FBbi:00000485

mTagBFP
type: Class
subclass of: Blue fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mTagBFP
created by: jm
creation date: 2010-03-17T02:16:38Z
has_obo_namespace: image
id: FBbi:00000486

AmCyanFP
type: Class
subclass of: Cyan fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of AmCyanFP
created by: jm
creation date: 2010-03-17T02:17:42Z
has_obo_namespace: image
id: FBbi:00000487

mCyFP
type: Class
subclass of: Cyan fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mCyFP
created by: jm
creation date: 2010-03-17T02:17:42Z
has_obo_namespace: image
id: FBbi:00000488

mTFP1
type: Class
subclass of: Cyan fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mTFP1
created by: jm
creation date: 2010-03-17T02:17:42Z
has_obo_namespace: image
id: FBbi:00000489

TagCFP
type: Class
subclass of: Cyan fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TagCFP
created by: jm
creation date: 2010-03-17T02:17:42Z
has_obo_namespace: image
id: FBbi:00000490

AQ143
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of AQ143
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000491

HcRed-tandemFP
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of HcRed-tandemFP
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000492

KatushkaFP
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of KatushkaFP
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000493

mKateFP
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mKateFP
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000494

mKate2FP
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mKate2FP
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000495

mPlumFP
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mPlumFP
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000496

tdKatuskaFP
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of tdKatuskaFP
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000497

tdRFP639
type: Class
subclass of: Far-red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of tdRFP639
created by: jm
creation date: 2010-03-17T02:19:04Z
has_obo_namespace: image
id: FBbi:00000498

AceFP
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of AceFP
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000499

Azami GreenFP
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of Azami GreenFP
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000500

CopGFP
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of CopGFP
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000501

mWasabiFP
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mWasabiFP
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000502

TagGFP
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TagGFP
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000503

TagGFP2
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TagGFP2
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000504

ZsGreenFP
type: Class
subclass of: Green fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of ZsGreenFP
created by: jm
creation date: 2010-03-17T02:20:00Z
has_obo_namespace: image
id: FBbi:00000505

DsRed-ExpressFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of DsRed-ExpressFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000506

DsRed-Express2FP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of DsRed-Express2FP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000507

DsRed-MaxFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of DsRed-MaxFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000508

DsRed-monomerFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of DsRed-monomerFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000509

DsRed2FP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of DsRed2FP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000510

dTomatoFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of dTomatoFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000511

Kusabira OrangeFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of Kusabira OrangeFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000512

Kusabira OrangeFP2
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of Kusabira OrangeFP2
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000513

mOrangeFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mOrangeFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000514

mOrange2FP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mOrange2FP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000515

TagRFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TagRFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000516

TagRFP-T
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TagRFP-T
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000517

tdTomatoFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of tdTomatoFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000518

turboRFP
type: Class
subclass of: Orange fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of turboRFP
created by: jm
creation date: 2010-03-17T02:22:53Z
has_obo_namespace: image
id: FBbi:00000519

AsRed2FP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of AsRed2FP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000520

eqFP611
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of eqFP611
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000521

HcRed1FP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of HcRed1FP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000522

JRedFP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of JRedFP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000523

mAppleFP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mAppleFP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000524

mCherryFP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mCherryFP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000525

mRasberryFP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mRasberryFP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000526

mRFP1
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mRFP1
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000527

mRubyFP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mRubyFP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000528

mStrawberryFP
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of mStrawberryFP
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000529

tdRFP611
type: Class
subclass of: Red fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of tdRFP611
created by: jm
creation date: 2010-03-17T02:24:26Z
has_obo_namespace: image
id: FBbi:00000530

PhiYFP
type: Class
subclass of: Yellow fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of PhiYFP
created by: jm
creation date: 2010-03-17T02:25:15Z
has_obo_namespace: image
id: FBbi:00000531

TagYFP
type: Class
subclass of: Yellow fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TagYFP
created by: jm
creation date: 2010-03-17T02:25:15Z
has_obo_namespace: image
id: FBbi:00000532

TurboYFP
type: Class
subclass of: Yellow fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of TurboYFP
created by: jm
creation date: 2010-03-17T02:25:15Z
has_obo_namespace: image
id: FBbi:00000533

ZsYellowFP
type: Class
subclass of: Yellow fluorescent proteins from Anthozoa
OBO foundry unique label: visualization of ZsYellowFP
created by: jm
creation date: 2010-03-17T02:25:15Z
has_obo_namespace: image
id: FBbi:00000534

fluorescent protein timer
type: Class
subclass of: optical highlighter
OBO foundry unique label: visualization of fluorescent protein timer
created by: jm
creation date: 2010-03-17T02:27:50Z
has_obo_namespace: image
id: FBbi:00000535

photoactivatable fluorescent protein
type: Class
subclass of: optical highlighter
OBO foundry unique label: visualization of photoactivatable fluorescent protein
created by: jm
creation date: 2010-03-17T02:27:50Z
has_obo_namespace: image
id: FBbi:00000536

photoconvertible fluorescent protein
type: Class
subclass of: optical highlighter
OBO foundry unique label: visualization of photoconvertible fluorescent protein
created by: jm
creation date: 2010-03-17T02:27:50Z
has_obo_namespace: image
id: FBbi:00000537

photoconvertible/photoswitchable fluorescent protein
type: Class
subclass of: optical highlighter
OBO foundry unique label: visualization of photoconvertible/photoswitchable fluorescent protein
created by: jm
creation date: 2010-03-17T02:27:50Z
has_obo_namespace: image
id: FBbi:00000538

photoswitchable fluorescent protein
type: Class
subclass of: optical highlighter
OBO foundry unique label: visualization of photoswitchable fluorescent protein
created by: jm
creation date: 2010-03-17T02:27:50Z
has_obo_namespace: image
id: FBbi:00000539

DsRed-ES FP
type: Class
subclass of: fluorescent protein timer
OBO foundry unique label: visualization of DsRed-ES FP
created by: jm
creation date: 2010-03-17T02:29:47Z
has_obo_namespace: image
id: FBbi:00000540

Fast-FT
type: Class
subclass of: fluorescent protein timer
OBO foundry unique label: visualization of Fast-FT
created by: jm
creation date: 2010-03-17T02:29:47Z
has_obo_namespace: image
id: FBbi:00000541

Medium-FT
type: Class
subclass of: fluorescent protein timer
OBO foundry unique label: visualization of Medium-FT
created by: jm
creation date: 2010-03-17T02:29:47Z
has_obo_namespace: image
id: FBbi:00000542

Slow-FT
type: Class
subclass of: fluorescent protein timer
OBO foundry unique label: visualization of Slow-FT
created by: jm
creation date: 2010-03-17T02:29:47Z
has_obo_namespace: image
id: FBbi:00000543

PA-GFP
type: Class
subclass of: photoactivatable fluorescent protein
OBO foundry unique label: visualization of PA-GFP
created by: jm
creation date: 2010-03-17T02:31:26Z
has_obo_namespace: image
id: FBbi:00000544

PA-CFP
type: Class
subclass of: photoactivatable fluorescent protein
OBO foundry unique label: visualization of PA-CFP
created by: jm
creation date: 2010-03-17T02:31:26Z
has_obo_namespace: image
id: FBbi:00000545

PA-mCherry1FP
type: Class
subclass of: photoactivatable fluorescent protein
OBO foundry unique label: visualization of PA-mCherry1FP
created by: jm
creation date: 2010-03-17T02:31:26Z
has_obo_namespace: image
id: FBbi:00000546

PA-mRFP
type: Class
subclass of: photoactivatable fluorescent protein
OBO foundry unique label: visualization of PA-mRFP
created by: jm
creation date: 2010-03-17T02:31:26Z
has_obo_namespace: image
id: FBbi:00000547

Phamret
type: Class
subclass of: photoactivatable fluorescent protein
OBO foundry unique label: visualization of Phamret
created by: jm
creation date: 2010-03-17T02:31:26Z
has_obo_namespace: image
id: FBbi:00000548

Dendra2FP
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of Dendra2FP
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000549

dEOSFP
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of dEOSFP
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000550

KaedeFP
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of KaedeFP
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000551

mEOS2FP
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of mEOS2FP
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000552

mKikGR
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of mKikGR
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000553

wtEOSFP
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of wtEOSFP
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000554

wtKIikGR
type: Class
subclass of: photoconvertible fluorescent protein
OBO foundry unique label: visualization of wtKIikGR
created by: jm
creation date: 2010-03-17T02:32:35Z
has_obo_namespace: image
id: FBbi:00000555

IrisFP
type: Class
subclass of: photoconvertible/photoswitchable fluorescent protein
OBO foundry unique label: visualization of IrisFP
created by: jm
creation date: 2010-03-17T02:32:44Z
has_obo_namespace: image
id: FBbi:00000556

bsDronpa
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of bsDronpa
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000557

Dronpa
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of Dronpa
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000558

Dronpa-3
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of Dronpa-3
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000559

E2GFP
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of E2GFP
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000560

KFP1
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of KFP1
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000561

mTFP0.7
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of mTFP0.7
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000562

PadronFP
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of PadronFP
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000563

rsCherryFP
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of rsCherryFP
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000564

rsCherryRevFP
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of rsCherryRevFP
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000565

rsFastLimeFP
type: Class
subclass of: photoswitchable fluorescent protein
OBO foundry unique label: visualization of rsFastLimeFP
created by: jm
creation date: 2010-03-17T02:34:12Z
has_obo_namespace: image
id: FBbi:00000566

optically-dense stain
type: Class
subclass of: stain with broad specificity
OBO foundry unique label: visualization of optically-dense stain
created by: jm
creation date: 2010-04-27T10:29:56Z
has_obo_namespace: image
id: FBbi:00000567

electron-dense stain
type: Class
subclass of: stain with broad specificity
OBO foundry unique label: visualization of electron-dense stain
created by: jm
creation date: 2010-04-27T10:29:56Z
has_obo_namespace: image
id: FBbi:00000568

uranyl salt
type: Class
subclass of: electron-dense stain
OBO foundry unique label: visualization of uranyl salt
created by: jm
creation date: 2010-04-27T10:38:31Z
has_obo_namespace: image
id: FBbi:00000569

lead salt
type: Class
subclass of: electron-dense stain
OBO foundry unique label: visualization of lead salt
created by: jm
creation date: 2010-04-27T10:38:31Z
has_obo_namespace: image
id: FBbi:00000570

osmium tetroxide
type: Class
subclass of: electron-dense stain
OBO foundry unique label: visualization of osmium tetroxide
created by: jm
creation date: 2010-04-27T10:38:31Z
has_obo_namespace: image
id: FBbi:00000571

potassium permanganate
type: Class
subclass of: electron-dense stain
OBO foundry unique label: visualization of potassium permanganate
created by: jm
creation date: 2010-04-27T10:38:31Z
has_obo_namespace: image
id: FBbi:00000572

uranium compound
type: Class
subclass of: negative staining
created by: jm
creation date: 2010-04-27T10:39:43Z
has_obo_namespace: image
id: FBbi:00000573

molybdenum compound
type: Class
subclass of: negative staining
created by: jm
creation date: 2010-04-27T10:39:43Z
has_obo_namespace: image
id: FBbi:00000574

tungsten compound
type: Class
subclass of: negative staining
created by: jm
creation date: 2010-04-27T10:39:43Z
has_obo_namespace: image
id: FBbi:00000575

aurothioglucose
type: Class
subclass of: negative staining
created by: jm
creation date: 2010-04-27T10:39:43Z
has_obo_namespace: image
id: FBbi:00000576

other negative stain
type: Class
subclass of: negative staining
created by: jm
creation date: 2010-04-28T06:06:52Z
has_obo_namespace: image
id: FBbi:00000577

other radioisotope
type: Class
subclass of: metabolically incorporated radioisotope
OBO foundry unique label: visualization of metabolically incorporated other radioisotope
created by: jm
creation date: 2010-04-28T06:08:02Z
has_obo_namespace: image
id: FBbi:00000578

isolated subcellular component
type: Class
subclass of: sample preparation method
definition: A fragment of a cell, subcellular organelle, or macromolecular complex.
created by: jm
creation date: 2010-04-28T06:08:42Z
has_obo_namespace: image
id: FBbi:00000579

secondary electron generation
type: Class
subclass of: imaged parameter
definition: electrons generated by inelastic scattering of other radiation, the primary radiation.
created by: jm
creation date: 2010-05-04T12:25:14Z
has_obo_namespace: image
id: FBbi:00000580

critical_point dried specimen
type: Class
subclass of: cryofixed tissue
definition: specimen from which water has been removed by a process that avoids liquid-gas and solid-gas phase transitions.
created by: jm
creation date: 2010-05-04T12:31:12Z
has_obo_namespace: image
id: FBbi:00000581

unprocessed raw data
type: Class
subclass of: computational method
definition: data as acquired, with no alterations that change the pixel values.
created by: jm
creation date: 2010-05-04T12:42:17Z
has_obo_namespace: image
id: FBbi:00000582

lyophilized specimen
type: Class
subclass of: cryofixed tissue
definition: specimen from which water has been removed by evaporation under vacuum at a temperature below freezing.
created by: jm
creation date: 2010-05-04T12:49:31Z
has_obo_namespace: image
id: FBbi:00000583

X-Rhodamine
type: Class
subclass of: fluorescent label
definition: fluorophore derivative of rhodamine with ex/em 580/605
OBO foundry unique label: visualization of X-Rhodamine conjugated to probe
created by: jm
creation date: 2010-05-04T09:02:54Z
has_obo_namespace: image
id: FBbi:00000584

serial block face SEM (SBFSEM)
type: Class
subclass of: back-scattered_electron imaging
definition: A method of reconstructing 3D structure by combining serial sectioning with scanning EM.
created by: jm
creation date: 2010-09-02T05:10:33Z
has_obo_namespace: image
id: FBbi:00000585

Axiom
annotated source: serial block face SEM (SBFSEM)
annotated property: definition
annotated target: A method of reconstructing 3D structure by combining serial sectioning with scanning EM.
database_cross_reference: PMID:15514700

elastic scattering of electrons
type: Class
subclass of: elastic scattering
created by: jm
creation date: 2010-09-03T08:42:47Z
has_obo_namespace: image
id: FBbi:00000586

elastic scattering of photons
type: Class
subclass of: elastic scattering
created by: jm
creation date: 2010-09-03T08:42:47Z
has_obo_namespace: image
id: FBbi:00000587

inelastic scattering of electrons
type: Class
subclass of: inelastic scattering
created by: jm
creation date: 2010-09-03T08:43:42Z
has_obo_namespace: image
id: FBbi:00000588

inelastic scattering of photons (Raman scattering)
type: Class
subclass of: inelastic scattering
created by: jm
creation date: 2010-09-03T08:43:42Z
has_obo_namespace: image
id: FBbi:00000589

source of contrast
type: Class
subclass of: method involved in biological imaging
definition: The source of the variation in the imaged parameter across the field of view.
created by: jm
creation date: 2010-09-03T08:53:13Z
has_obo_namespace: image
id: FBbi:00000590

differences in chemical composition
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000591

distribution of epitope
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000592

form birefringence
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000593

intrinsic birefringence
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000594

stress-induced birefringence
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000595

distribution of a specific nucleic acid sequence
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000596

distribution of a specific protein
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000597

differences in adsorption or binding of stain
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000598

boundaries between regions with different refractive index
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000599

differences in amount of elastic light scattering
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-03T09:55:12Z
has_obo_namespace: image
id: FBbi:00000600

differences in deposition of metal shadow
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-04T11:57:06Z
has_obo_namespace: image
id: FBbi:00000601

differences in intrinsic optical density
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-04T12:55:54Z
has_obo_namespace: image
id: FBbi:00000602

fluorescence polarization microscopy
type: Class
subclass of: fluorescence microscopy
created by: jm
creation date: 2010-09-04T01:28:20Z
has_obo_namespace: image
id: FBbi:00000603

compartmentalization of stain or label
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-04T01:31:54Z
has_obo_namespace: image
id: FBbi:00000604

differences in fluorescence lifetime
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-04T01:35:37Z
has_obo_namespace: image
id: FBbi:00000605

differences in orientation of fluorophore
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-04T01:36:45Z
has_obo_namespace: image
id: FBbi:00000606

intrinsic mass distribution
type: Class
subclass of: source of contrast
created by: jm
creation date: 2010-09-04T01:51:14Z
has_obo_namespace: image
id: FBbi:00000607

X-ray fluorescence
type: Class
subclass of: fluorescence emission
created by: jm
creation date: 2010-09-04T02:05:02Z
has_obo_namespace: image
id: FBbi:00000608

heat fixed tissue
type: Class
subclass of: fixation method
created by: jm
creation date: 2010-09-04T11:49:25Z
has_obo_namespace: image
id: FBbi:00000609

copper salt
type: Class
subclass of: electron-dense stain
OBO foundry unique label: visualization of copper salt
created by: jm
creation date: 2010-09-04T11:56:02Z
has_obo_namespace: image
id: FBbi:00000610

dispersed cells in vitro
type: Class
subclass of: sample preparation method
created by: jm
creation date: 2010-09-28T04:35:54Z
has_obo_namespace: image
id: FBbi:00000611

fluorescent protein derived from Arabidopsis
type: Class
subclass of: fluorescent protein tag
OBO foundry unique label: visualization of fluorescent protein derived from Arabidopsis
created by: jm
creation date: 2011-05-23T09:33:44Z
has_obo_namespace: image
id: FBbi:00000612

vidicon tube camera
type: Class
subclass of: area detector
created by: jm
creation date: 2011-05-23T09:49:58Z
has_obo_namespace: image
id: FBbi:00000613

phototropin 2
type: Class
subclass of: fluorescent protein derived from Arabidopsis
OBO foundry unique label: visualization of phototropin 2
created by: jm
creation date: 2011-05-23T09:55:54Z
has_obo_namespace: image
id: FBbi:00000614

miniSOG
type: Class
subclass of: phototropin 2
OBO foundry unique label: visualization of miniSOG
created by: jm
creation date: 2011-05-23T09:57:01Z
has_obo_namespace: image
id: FBbi:00000615

evanescent wave scattering
type: Class
subclass of: dark-field microscopy
created by: jm
creation date: 2011-05-23T10:09:41Z
has_obo_namespace: image
has_related_synonym: FTIR frustrated total internal reflection
id: FBbi:00000616

evanescent wave microscopy
type: Class
subclass of: fluorescence microscopy
created by: jm
creation date: 2011-05-23T10:10:58Z
has_obo_namespace: image
has_related_synonym: total internal reflection fluorescence TIRF
id: FBbi:00000617

ground state depletion scanning (GSD)
type: Class
subclass of: resolution-enhancing method
created by: jm
creation date: 2011-05-23T10:34:07Z
has_obo_namespace: image
id: FBbi:00000618

nearfield illumination
type: Class
subclass of: illumination method
subclass of: Restriction
  on property: makes_use_of
  some values from: evanescent wave microscopy
created by: jm
creation date: 2011-05-23T10:43:15Z
has_obo_namespace: image
id: FBbi:00000619

nearfield illumination
type: Class
subclass of: illumination method
subclass of: Restriction
  on property: makes_use_of
  some values from: evanescent wave scattering
created by: jm
creation date: 2011-05-23T10:44:03Z
has_obo_namespace: image
id: FBbi:00000620

freeze-substituted tissue
type: Class
subclass of: cryofixed tissue
created by: jm
creation date: 2011-05-23T10:51:16Z
has_obo_namespace: image
id: FBbi:00000621

high-voltage electron microscopy (HVEM)
type: Class
subclass of: transmission electron microscopy (TEM)
created by: jm
creation date: 2011-05-23T10:53:45Z
has_obo_namespace: image
id: FBbi:00000622

intermediate voltage electron microacopy (IVEM)
type: Class
subclass of: transmission electron microscopy (TEM)
created by: jm
creation date: 2011-05-23T10:53:45Z
has_obo_namespace: image
id: FBbi:00000623

radiography
type: Class
equivalent class: Class
  intersection of: recorded image
  intersection of: Restriction
    on property: makes_use_of
    some values from: x-ray/gamma ray illumination
subclass of: recorded image
subclass of: Restriction
  on property: makes_use_of
  some values from: x-ray/gamma ray illumination
definition: An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination.
has_obo_namespace: image
id: FBbi:00001000

Axiom
annotated source: radiography
annotated property: definition
annotated target: An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination.
database_cross_reference: http://en.wikipedia.org/w/index.php

X-ray radiography
type: Class
equivalent class: Class
  intersection of: recorded image
  intersection of: Restriction
    on property: makes_use_of
    some values from: X-ray illumination
subclass of: radiography
subclass of: Restriction
  on property: makes_use_of
  some values from: X-ray illumination
definition: Radiography using X-rays
has_exact_synonym: X-radiography
has_obo_namespace: image
has_related_synonym: X-ray
id: FBbi:00001001
in_subset: PhenoImageShare ImagingMethod

X-ray computed tomography
type: Class
equivalent class: Class
  intersection of: computed tomography
  intersection of: Restriction
    on property: makes_use_of
    some values from: X-ray illumination
subclass of: X-ray tomography
subclass of: computed tomography
database_cross_reference: MeSH:D014057
database_cross_reference: http://en.wikipedia.org/wiki/X-ray_computed_tomography
has_exact_synonym: CAT scan
has_exact_synonym: CT scan
has_exact_synonym: X-ray CT
has_obo_namespace: image
has_related_synonym: computed axial tomography
id: FBbi:00001002
in_subset: PhenoImageShare ImagingMethod

X-ray tomography
type: Class
equivalent class: Class
  intersection of: tomography
  intersection of: Restriction
    on property: makes_use_of
    some values from: X-ray illumination
subclass of: X-ray radiography
subclass of: tomography
definition: Tomography using X-ray illumination.
has_obo_namespace: image
id: FBbi:00001003

tomography
type: Class
subclass of: recorded image
definition: An imaging technique that creates virtual sections through the use of any kind of penetrating wave.
has_obo_namespace: image
id: FBbi:00001004

computed tomography
type: Class
subclass of: tomography
definition: Tomography in which virtual sections are taken from multiple angles and the results are processed via tomographic reconstruction software to produce 2 or 3D images.
has_obo_namespace: image
id: FBbi:00001005

x-ray/gamma ray illumination
type: Class
subclass of: illumination by photons
has_obo_namespace: image
id: FBbi:00001006

gamma ray illumination
type: Class
subclass of: x-ray/gamma ray illumination
has_obo_namespace: image
id: FBbi:00001007

fixation method
type: Class
subclass of: sample preparation method
has_obo_namespace: image
id: FBbi:00001012

focussed ion beam scanning electron microscopy (FIB-SEM)
type: Class
subclass of: back-scattered_electron imaging
definition: A method of reconstructing 3D structure by combining focussed ion beam milling to remove sucessive layers from a sample block with scanning EM to image the exposed surface between each milling step.
has_exact_synonym: FIB-SEM
has_obo_namespace: image
id: FBbi:00050000

Axiom
annotated source: focussed ion beam scanning electron microscopy (FIB-SEM)
annotated property: definition
annotated target: A method of reconstructing 3D structure by combining focussed ion beam milling to remove sucessive layers from a sample block with scanning EM to image the exposed surface between each milling step.
database_cross_reference: PMID:22119321

method involved in biological imaging
type: Class
subclass of: Thing
has_obo_namespace: image
id: FBbi_root:00000000

molecular_function
type: Class
subclass of: process
OBO foundry unique label: molecular process

catalytic activity
type: Class
subclass of: molecular_function

biological_process
type: Class
subclass of: process

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

Imp
comment: This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: occurs in
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x