image 1.2 Biological Imaging Methods CV This CV covers sample preparation, visualization and imaging methods. corrections and additions to chris@bio.umass.edu editor:Chris Woodcock (The Cell: An Image Library) definition OBO foundry unique label 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 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. is a defining property chain axiom where second argument is reflexive A small set of imaging methods for use in PhenoImageShare indexes subset_property database_cross_reference has_exact_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole 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. 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 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'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part 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. 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 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'. has_part has part preceded by 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. 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. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes 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. precedes 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 occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [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 Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process The child is an essential component of the parent device, or plays an essential role in performance of the parent function. jm 2010-03-09T09:32:04Z image FBbi:00000346 makes_use_of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant 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. dos 2017-05-24T09:30:46Z has regulatory component activity 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. dos 2017-05-24T09:31:01Z 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 negative regulatory component activity 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. dos 2017-05-24T09:31:17Z 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 positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity 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. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z 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. directly regulated by 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. GOC:dos 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. dos 2017-09-17T13:52:38Z directly negatively regulated by 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. GOC:dos 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. dos 2017-09-17T13:52:47Z directly positively regulated by 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. GOC:dos 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. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity 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. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true 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. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. 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. has component 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 Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan This is the transitive form of the develops from relation develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into 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. 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 Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates 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. Chris Mungall negatively regulates (process to process) negatively regulates 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. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' 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. Chris Mungall has function realized in 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)". RO_0000053 some (RO_0000054 only ?Y) capable of 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. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true Chris Mungall 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. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to 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. Chris Mungall consumes has input Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall has developmental contribution from inverse of has developmental contribution from Chris Mungall developmentally contributes to 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 false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by 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. 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 A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. 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. affects acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by cjm 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, positive effect cjm 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 causally upstream of, negative effect A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing 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. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall input of 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). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes 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 yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of 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. Chris Mungall immediately causally upstream of 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. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of 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 OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. 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. Chris Mungall executes activity in enables activity in is active in true 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. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' 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. Chris Mungall 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. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations 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. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates 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. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of 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. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of 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. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 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. Chris Mungall has part that occurs in true Chris Mungall is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process 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. Chris Mungall 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 processes 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 Chris Mungall 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 Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property 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). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences 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. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' 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 Chris Mungall has part structure that is capable of 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. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent 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. directly positively regulates (process to process) directly positively regulates 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. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect 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 cjm 2018-01-26T23:53:14Z acts upstream of, positive effect 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 cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect 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. Vasundra Touré regulates activity of 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. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity anatomical entity biological entity jm 2010-03-07T02:05:26Z image FBbi:00000000 dummy term true image FBbi:00000001 sample preparation method image FBbi:00000002 chemically fixed tissue image FBbi:00000003 coagulating-fixative fixed tissue image FBbi:00000004 acetone fixed tissue image FBbi:00000005 acrolein fixed tissue image FBbi:00000006 ethanol fixed tissue image FBbi:00000007 methanol fixed tissue image FBbi:00000008 crosslinking-fixative fixed tissue image EGS FBbi:00000009 ethylene glycol-bis-succinimidyl succinate fixed tissue image FBbi:00000010 formaldehyde fixed tissue image FBbi:00000011 glutaraldehyde fixed tissue image FBbi:00000012 osmium tetroxide fixed tissue image FBbi:00000013 cryofixed tissue image FBbi:00000014 unfixed tissue image FBbi:00000015 embedded tissue image FBbi:00000016 tissue in plastic embedment image FBbi:00000017 tissue in acrylic resin embedment image FBbi:00000018 tissue in epoxy resin embedment image FBbi:00000019 tissue in wax embedment image FBbi:00000020 tissue in paraffin embedment image FBbi:00000021 tissue in polyester wax embedment image FBbi:00000022 tissue in polyethylene glycol embedment image FBbi:00000023 unembedded tissue image FBbi:00000024 whole mounted tissue Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state. image live-cell imaging FBbi:00000025 living tissue Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state. XX:ISBN978-087969683-2 image FBbi:00000026 sectioned tissue image FBbi:00000027 cryostat-sectioned tissue image FBbi:00000028 hand-sectioned tissue image FBbi:00000029 microtome-sectioned tissue image FBbi:00000030 vibratome-sectioned tissue image FBbi:00000031 visualization method image FBbi:00000032 endogenous substrate, non-vital dye true image FBbi:00000033 diagram visualization of HA peptide tag image FBbi:00000034 HA peptide tag visualization of cresyl fast violet image FBbi:00000035 cresyl fast violet image FBbi:00000036 endogenous substrate, diaminobenzidine true 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. visualization of eosin image FBbi:00000037 eosin 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. Wikipedia:http://en.wikipedia.org/wiki/H%26E_stain visualization of ethidium bromide image FBbi:00000038 ethidium bromide visualization of fuchsin image FBbi:00000039 fuchsin visualization of giemsa image FBbi:00000040 giemsa 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. visualization of hematoxylin image FBbi:00000041 hematoxylin 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. Wikipedia:http://en.wikipedia.org/wiki/H%26E_stain visualization of methyl green image FBbi:00000042 methyl green visualization of methyl violet image FBbi:00000043 methyl violet visualization of nitro blue tetrazolium chloride image FBbi:00000044 nitro blue tetrazolium chloride visualization of nuclear fast red image FBbi:00000045 nuclear fast red visualization of orcein image FBbi:00000046 orcein visualization of propidium iodide image PI FBbi:00000047 propidium iodide visualization of SYTOX Green image FBbi:00000048 SYTOX Green visualization of toluidine blue image FBbi:00000049 toluidine blue image FBbi:00000050 endogenous substrate, vital dye true visualization of acridine orange image AO FBbi:00000051 acridine orange visualization of Hoechst 33342 image HO342 Hoechst 33342 FBbi:00000052 Hoechst 33342 visualization of cationic colloidal gold image FBbi:00000053 cationic colloidal gold visualization of CMX rosamine (Mitotracker Red) image Mitotracker X FBbi:00000054 CMX rosamine (Mitotracker Red) visualization of DiOC6 (3,3'-dihexyloxacarbocyanine iodide) image DiOC FBbi:00000055 DiOC6 (3,3'-dihexyloxacarbocyanine iodide) visualization of 4',6-diamidino-2-phenylindole (DAPI) image DAPI FBbi:00000056 4',6-diamidino-2-phenylindole (DAPI) image FBbi:00000057 lucifer yellow visualization of methylene blue image FBbi:00000058 methylene blue visualization of Nile blue A image FBbi:00000059 Nile blue A visualization of Nile red image FBbi:00000060 Nile red visualization of pyronine image FBbi:00000061 pyronine visualization of rhodamine 123 image FBbi:00000062 rhodamine 123 visualization of rhodamine B image FBbi:00000063 rhodamine B visualization of SYTO Blue image FBbi:00000064 SYTO Blue visualization of SYTO Green image FBbi:00000065 SYTO Green visualization of SYTO Orange image FBbi:00000066 SYTO Orange visualization of SYTO Red image FBbi:00000067 SYTO Red visualization of YO-PRO-1 image FBbi:00000068 YO-PRO-1 image FBbi:00000069 endogenous substrate, dye conjugate true image LysoTracker FBbi:00000070 endogenous substrate, acidotropic-fluor conjugate true image FBbi:00000071 endogenous substrate, lectin-fluor conjugate true image FBbi:00000072 endogenous substrate, lectin-gold conjugate true visualization of taxol image FBbi:00000073 taxol image FBbi:00000074 endogenous substrate, phalloidin-fluor conjugate true image FBbi:00000075 exogenous label true visualization of genetically encoded enzyme image FBbi:00000076 genetically encoded enzyme visualization of beta-galactosidase image lacZ, X-gal FBbi:00000077 beta-galactosidase visualization of beta-glucuronidase image GUS, X-gluc FBbi:00000078 beta-glucuronidase visualization of genetically encoded tag image FBbi:00000079 genetically encoded tag visualization of EBFP image BFP FBbi:00000080 EBFP visualization of ECFP image CFP FBbi:00000081 ECFP visualization of EGFP image GFP FBbi:00000082 EGFP image RFP FBbi:00000083 Aequorea victoria red fluorescent protein tag true visualization of EYFP image YFP FBbi:00000084 EYFP visualization of DsRed image DsRed FBbi:00000085 DsRed visualization of c-MYC peptide tag image FBbi:00000086 c-MYC peptide tag visualization of FLAG peptide tag image FBbi:00000087 FLAG peptide tag visualization of the connected regions of a cell by filling with a label image FBbi:00000088 intracellular filling Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C jm 2010-03-07T02:05:48Z image tissue in amorphous ice embedment FBbi:00000089 tissue in vitreous ice embedment Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C PMID:3043536 image FBbi:00000090 fluor labeled RNA fill image FBbi:00000091 5-SFX fluorescein RNA fill image FBbi:00000092 X-rhodamine RNA fill Tissue treated to make cell membranes permeable, typically for the purpose of allowing access by exogenous stains or substrates. jm 2010-03-07T02:26:37Z image FBbi:00000093 permeabilized tissue image FBbi:00000094 fluor labeled protein fill image FBbi:00000095 fluor conjugated actin fill image FBbi:00000096 Alexa Fluor 488 actin fill true image FBbi:00000097 Alexa Fluor 568 actin fill true image FBbi:00000098 fluoresceine actin fill true image FBbi:00000099 rhodamine actin fill true visualization of phalloidin image FBbi:00000100 phalloidin image FBbi:00000101 Alexa Fluor 350 phalloidin fill true image FBbi:00000102 Alexa Fluor 488 phalloidin fill true image FBbi:00000103 eosin phalloidin fill true image FBbi:00000104 fluoresceine phalloidin fill true image FBbi:00000105 Oregon Green 488 phalloidin fill true image FBbi:00000106 Oregon Green 514 phalloidin fill true image FBbi:00000107 rhodamine phalloidin fill true image FBbi:00000108 Texas Red-X phalloidin fill true image FBbi:00000109 fluor conjugated tubulin fill image FBbi:00000110 Oregon Green 514 tubulin fill true image FBbi:00000111 X-rhodamine tubulin fill true visualization of probe for lipid image FBbi:00000112 probe for lipid visualization of DiA image FBbi:00000113 DiA visualization of DiD image FBbi:00000114 DiD visualization of DiI image FBbi:00000115 DiI visualization of DiO image FBbi:00000116 DiO visualization of DiR image FBbi:00000117 DiR image FBbi:00000118 miscellaneous fill image Neurobiotin FBbi:00000119 biotin ethylenediamine fill image FBbi:00000120 cobalt fill image FBbi:00000121 silver-intensified cobalt fill visualization of metabolically incorporated radioisotope image FBbi:00000122 metabolically incorporated radioisotope visualization of metabolically incorporated [14]C image FBbi:00000123 [14]C visualization of metabolically incorporated [32]P image FBbi:00000124 [32]P visualization of metabolically incorporated [33]P image FBbi:00000125 [33]P visualization of metabolically incorporated [35]S image FBbi:00000126 [35]S visualization of metabolically incorporated [3]H image FBbi:00000127 [3]H image FBbi:00000128 vizualization of label conjugated to probe tissue made permeable by the action of glycerol jm 2010-03-07T02:37:12Z image glycerinated tissue FBbi:00000129 glycerol permeabilized visualization of labeled primary antibody image FBbi:00000130 labeled primary antibody image FBbi:00000131 primary antibody-enzyme conjugate, substrate true visualization of alkaline phosphatase conjugated to probe image FBbi:00000132 alkaline phosphatase image FBbi:00000133 primary antibody-alkaline phosphastase conjugate, DAB true image FBbi:00000134 primary antibody-alkaline phosphastase conjugate, ELF 97 phosphate true image FBbi:00000135 primary antibody-alkaline phosphastase conjugate, Vector Black true image FBbi:00000136 primary antibody-alkaline phosphastase conjugate, Vector Blue true image FBbi:00000137 primary antibody-alkaline phosphastase conjugate, Vector Red true visualization of horseradish peroxidase conjugated to probe image FBbi:00000138 horseradish peroxidase image FBbi:00000139 primary antibody-horseradish peroxidase, 4-chloro-1-naphthol true image FBbi:00000140 primary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole true image FBbi:00000141 primary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine true image FBbi:00000142 primary antibody-horseradish peroxidase, Vector NovaRed true image FBbi:00000143 primary antibody-horseradish peroxidase, Vector SG true image FBbi:00000144 primary antibody-horseradish peroxidase, Vector VIP true image FBbi:00000145 primary antibody-fluor conjugate true image AMCA FBbi:00000146 primary antibody-aminomethylcoumarin acetate true image FBbi:00000147 primary antibody-Cascade blue true image Cy2 FBbi:00000148 primary antibody-cyanine true image FITC FBbi:00000149 primary antibody-fluorescein isothiocyanate true image Cy3 FBbi:00000150 primary antibody-indocarbocyanine true image Cy5 FBbi:00000151 primary antibody-indodicarbocyanine true image RRX FBbi:00000152 primary antibody-rhodamine red-X true image TRITC FBbi:00000153 primary antibody-tetramethyl rhodamine isothiocyanate true image TR FBbi:00000154 primary antibody-Texas Red true image FBbi:00000155 primary antibody-gold conjugate true visualization of primary antibody plus labeled secondary antibody image FBbi:00000156 primary antibody plus labeled secondary antibody image FBbi:00000157 secondary antibody-enzyme conjugate, substrate true visualization of acid phosphatase conjugated to probe image FBbi:00000158 acid phosphatase image FBbi:00000159 secondary antibody-alkaline phosphastase conjugate, DAB true image FBbi:00000160 secondary antibody-alkaline phosphastase conjugate, ELF 97 phosphate true image FBbi:00000161 secondary antibody-alkaline phosphastase conjugate, Fast Blue B true image FBbi:00000162 secondary antibody-alkaline phosphastase conjugate, Fast Red true image FBbi:00000163 secondary antibody-alkaline phosphastase conjugate, INT true image FBbi:00000164 secondary antibody-alkaline phosphastase conjugate, Magenta Phos true image FBbi:00000165 secondary antibody-alkaline phosphastase conjugate, NABP true image FBbi:00000166 secondary antibody-alkaline phosphastase conjugate, NAGP true image FBbi:00000167 secondary antibody-alkaline phosphastase conjugate, NAMP true image FBbi:00000168 secondary antibody-alkaline phosphastase conjugate, NATP true image FBbi:00000169 secondary antibody-alkaline phosphastase conjugate, NBT true image FBbi:00000170 secondary antibody-alkaline phosphastase conjugate, Vector Black true image FBbi:00000171 secondary antibody-alkaline phosphastase conjugate, Vector Blue true image FBbi:00000172 secondary antibody-alkaline phosphastase conjugate, Vector Red true image FBbi:00000173 secondary antibody-alkaline phosphastase conjugate, BCIP true image FBbi:00000174 secondary antibody-beta-galactosidase, X-Gal true image FBbi:00000175 secondary antibody-beta-glucuronidase, X-gluc true visualization of esterase conjugated to probe image FBbi:00000176 esterase image FBbi:00000177 secondary antibody-esterase, Naphthol-AS-D-chloroacetate true visualization of glucose oxidase conjugated to probe image FBbi:00000178 glucose oxidase image FBbi:00000179 secondary antibody-glucose oxidase, TNBT true image FBbi:00000180 secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine true image FBbi:00000181 secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine silver enhanced true image FBbi:00000182 secondary antibody-horseradish peroxidase, 4-chloro-1-naphthol true image FBbi:00000183 secondary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole true image FBbi:00000184 secondary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine true image FBbi:00000185 secondary antibody-horseradish peroxidase, Vector NovaRed true image FBbi:00000186 secondary antibody-horseradish peroxidase, Vector SG true image FBbi:00000187 secondary antibody-horseradish peroxidase, Vector VIP true image FBbi:00000188 secondary antibody-phosphatase, Naphthol-AS-BI-phosphate true image FBbi:00000189 secondary antibody-fluor conjugate true image FBbi:00000190 secondary antibody-Alexa Fluor conjugate true visualization of aminomethylcoumarin conjugated to probe image AMCA FBbi:00000191 aminomethylcoumarin visualization of Cascade blue conjugated to probe image FBbi:00000192 Cascade blue image Cy2 FBbi:00000193 secondary antibody-cyanine conjugate true image DTAF FBbi:00000194 secondary antibody-diaminotriazinylaminoflorescein conjugate true image FITC FBbi:00000195 secondary antibody-fluorescein isothiocyanate conjugate true image Cy3 FBbi:00000196 secondary antibody-indocarbocyanine conjugate true image Cy5 FBbi:00000197 secondary antibody-indodicarbocyanine conjugate true image LSRC FBbi:00000198 secondary antibody-lissamine rhodamine sulfonyl chloride true image RRX FBbi:00000199 secondary antibody-rhodamine red-X conjugate true image TRITC FBbi:00000200 secondary antibody-tetramethyl rhodamine isothiocyanate conjugate true image TR FBbi:00000201 secondary antibody-Texas red conjugate true visualization of gold conjugated to probe image FBbi:00000202 gold image FBbi:00000203 labeled nucleic acid probe true visualization of DNA probe image FBbi:00000204 DNA probe image FBbi:00000205 biotin labeled DNA probe true image FBbi:00000206 digoxigenin labeled DNA probe true image FBbi:00000207 fluor labeled DNA probe true image FBbi:00000208 BODIPY TR-14-dUTP labeled DNA probe true image FBbi:00000209 bromodeoxyuridine labeled DNA probe true image FBbi:00000210 fluoresceine-12-dUTP labeled DNA probe true image FBbi:00000211 Oregon Green 488-5-dUTP labeled DNA probe true image FBbi:00000212 radioisotope labeled DNA probe true image FBbi:00000213 [32]P labeled DNA probe true image FBbi:00000214 [33]P labeled DNA probe true visualization of RNA probe image FBbi:00000215 RNA probe image FBbi:00000216 biotin labeled RNA probe true image FBbi:00000217 digoxigenin labeled RNA probe true image FBbi:00000218 fluoroscein labeled RNA probe true image FBbi:00000219 radioisotope labeled RNA probe true image FBbi:00000220 [32]P labeled RNA probe true image FBbi:00000221 [33]P labeled RNA probe true image FBbi:00000222 imaging method image FBbi:00000223 graphic illustration image FBbi:00000224 computer graphic image FBbi:00000225 black and white graphic image FBbi:00000226 color graphic image FBbi:00000227 grey scale graphic image FBbi:00000228 camera lucida assisted graphic image FBbi:00000229 free hand graphic image FBbi:00000230 line art graphic image FBbi:00000231 charcoal pencil graphic image FBbi:00000232 colored pencil graphic image FBbi:00000233 graphite pencil graphic image black and white graphic FBbi:00000234 pen and ink graphic image FBbi:00000235 painted graphic image FBbi:00000236 acrylic painted graphic image FBbi:00000237 oil painted graphic image FBbi:00000238 pastel painted graphic image FBbi:00000239 watercolor painted graphic methods for imaging objects large enough to be observed by the unaided eye image FBbi:00000240 macroscopy methods for forming images of objects too small to be observed with the unaided eye image FBbi:00000241 microscopy image FBbi:00000242 wide field light micrograph true image FBbi:00000243 bright-field microscopy imaging with rejection of the unscattered illumination (removal of the zero order component of the diffracted wave) image FBbi:00000244 dark-field microscopy image DIC Nomarski FBbi:00000245 differential interference contrast microscopy image FBbi:00000246 fluorescence microscopy image FBbi:00000247 phase contrast microscopy image FBbi:00000248 polarization microscopy image FBbi:00000249 time lapse microscopy image FBbi:00000250 narrow field light micrograph true image FBbi:00000251 confocal microscopy image FBbi:00000252 single-spot confocal microscopy image FBbi:00000253 spinning disk confocal microscopy image FBbi:00000254 two-photon laser scanning microscopy image FBbi:00000255 multi-photon microscopy image mode of electron microscopy FBbi:00000256 electron microscopy image is formed by scanning the surface of the specimen with a beam of electrons in a raster pattern image FBbi:00000257 scanning electron microscopy (SEM) image FBbi:00000258 transmission electron microscopy (TEM) the scanning probe is maintained at a fixed distance above the surface e of the specimen by van der Waals forces image FBbi:00000259 atomic force microscopy http://en.wikipedia.org/wiki/X-ray_microscope image FBbi:00000260 X-ray microscopy image FBbi:00000261 montage Membrane permeabilization by the action of ionic or non-ionic detergents jm 2010-03-07T02:37:21Z image FBbi:00000262 detergent permeabilized permeabilization due to extraction of lipid from membranes by an organic solvent such as acetone or methanol. jm 2010-03-07T02:37:29Z image FBbi:00000263 solvent permeabilized Saponin, a detergent-like molecule, preferentially forms holes in membranes that contain cholesterol. jm 2010-03-07T02:43:41Z image saponized tissue FBbi:00000264 saponin permeabilized methods and devices used for capturing an image of a real object; distinct from images created by artwork image recording method jm 2010-03-09T09:57:38Z image photograph FBbi:00000265 recorded image methods and devices used for creating images by some form of artwork, as distinct from capturing images by means of some recording device image portrayal method jm 2010-03-09T10:04:40Z image artwork drawing FBbi:00000266 portrayed image A form of graphical illustration that changes with time to give a sense of motion or represent dynamic changes in the portrayal. jm 2010-03-09T10:12:11Z image FBbi:00000267 animation sources and methods for illumination jm 2010-03-09T10:38:14Z image FBbi:00000268 illumination method media and devices employed for recording the alterations in the illumination that result from its interaction with the sample jm 2010-03-09T10:38:14Z image FBbi:00000269 detection method The physical property of the specimen that leads to the modifications of the illumination that are recorded in the image. jm 2010-03-09T10:38:14Z image FBbi:00000270 imaged parameter jm 2010-03-09T10:38:14Z image FBbi:00000271 contrast-enhancing method jm 2010-03-09T10:46:27Z image FBbi:00000272 illumination by photons jm 2010-03-09T10:46:27Z image FBbi:00000273 illumination by electrons jm 2010-03-09T10:46:27Z image FBbi:00000274 illumination by acoustic waves jm 2010-03-09T10:46:27Z image FBbi:00000275 illumination by neutrons jm 2010-03-09T10:46:27Z image FBbi:00000276 illumination by ions illumination that covers the entire field of view of the image-forming lens jm 2010-03-09T10:50:41Z image FBbi:00000277 widefield illumination illumination restricted to a small portion of the field of view of the imaging lens; often one or more diffraction limited spots jm 2010-03-09T10:50:41Z image FBbi:00000278 narrowfield illumination jm 2010-03-09T10:50:41Z image FBbi:00000279 coherent illumination jm 2010-03-09T10:50:41Z image FBbi:00000280 incoherent illumination jm 2010-03-09T10:50:41Z image FBbi:00000281 nearfield illumination jm 2010-03-09T10:50:41Z image FBbi:00000282 farfield illumination jm 2010-03-09T10:50:41Z image FBbi:00000283 continuous illumination illumination that varies with time; often achieved with pulsed lasers for the purpose of generating very-high peak illumination power jm 2010-03-09T10:50:41Z image FBbi:00000284 pulsed illumination jm 2010-03-09T10:50:41Z image FBbi:00000285 oblique illumination illumination by a single spot of light that is scanned across the field of view jm 2010-03-09T10:51:29Z image FBbi:00000286 single point scanning illumination by multiple points of light simultaneously jm 2010-03-09T10:51:29Z image FBbi:00000287 multiple point scanning scanning by multiple points of light arising from pinholes in a spinning disk that is illuminated by a widefield source jm 2010-03-09T10:52:38Z image FBbi:00000288 spinning disk scanning Multiple points of illumination generated by a fixed array of sources. jm 2010-03-09T10:52:38Z image FBbi:00000289 array scanning illumination parallel or at small angles to the optical axis is attenuated or blocked by a stop jm 2010-03-09T11:04:14Z image FBbi:00000290 hollow-cone illumination 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. jm 2010-03-09T11:04:14Z image FBbi:00000291 anaxial illumination 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. : illumination restricted to angles that exceed the acceptance angle of the image-forming lens jm 2010-03-09T11:04:41Z image FBbi:00000292 darkfield illumination 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 jm 2010-03-09T11:04:41Z image FBbi:00000293 Rheinberg illumination jm 2010-03-09T11:33:49Z image FBbi:00000294 charge coupled device (CCD) jm 2010-03-09T11:33:49Z image FBbi:00000295 photomultiplier tube (PMT) jm 2010-03-09T11:33:49Z image FBbi:00000296 photodiode jm 2010-03-09T11:33:49Z image FBbi:00000297 avalanche photodiode (APD) jm 2010-03-09T11:33:49Z image FBbi:00000298 silicon intensified target tube (SIT) jm 2010-03-09T11:33:49Z image FBbi:00000299 intensified SIT (ISIT) jm 2010-03-09T11:33:49Z image FBbi:00000300 intensified CCD (ICCD) jm 2010-03-09T11:33:49Z image FBbi:00000301 electron multiplying CCD (EMCCD) jm 2010-03-09T11:33:49Z image FBbi:00000302 electron bombardment CCD (EBCCD) jm 2010-03-09T11:33:49Z image FBbi:00000303 film jm 2010-03-09T11:33:49Z image FBbi:00000304 complementary metal oxide semiconductor (CMOS) jm 2010-03-09T11:33:49Z image FBbi:00000305 piezo-electric device jm 2010-03-09T12:45:35Z image FBbi:00000306 wide-field detection jm 2010-03-09T12:45:35Z image FBbi:00000307 narrow-field detection jm 2010-03-09T03:11:47Z image FBbi:00000308 absorption of illumination jm 2010-03-09T03:11:47Z image FBbi:00000309 inelastic scattering jm 2010-03-09T03:11:47Z image FBbi:00000310 elastic scattering jm 2010-03-09T03:11:47Z image FBbi:00000311 refractive index jm 2010-03-09T03:11:47Z image FBbi:00000312 optical path length gradient jm 2010-03-09T03:11:47Z image FBbi:00000313 retardance jm 2010-03-09T03:11:47Z image FBbi:00000314 stiffness jm 2010-03-09T03:11:47Z image FBbi:00000315 electron density jm 2010-03-09T03:11:47Z image FBbi:00000316 fluorescence emission jm 2010-03-09T03:11:47Z image FBbi:00000317 sub-nanosecond time-resolved fluorescence emission) jm 2010-03-09T03:11:47Z image FBbi:00000318 fluorescence polarization (polarization angle resolved fluorescence emission) jm 2010-03-09T03:11:47Z image FBbi:00000319 chemical composition jm 2010-03-09T03:11:47Z image FBbi:00000320 elevation methods for increasing the resolution beyond the classical Abbe diffraction limit jm 2010-03-09T03:12:34Z image FBbi:00000321 resolution-enhancing method optical contrast enhancing method jm 2010-03-09T03:14:53Z image FBbi:00000322 optical method computational contrast enhancing method jm 2010-03-09T03:14:53Z image FBbi:00000323 computational method jm 2010-03-09T03:20:14Z image FBbi:00000324 in-focus phase contrast jm 2010-03-09T03:20:14Z image FBbi:00000325 defocus phase contrast a birefringent optical element typically used to split polarized illumination into two sets of parallel but displaced rays jm 2010-03-09T03:20:14Z image FBbi:00000326 Wollaston prism jm 2010-03-09T03:20:14Z image FBbi:00000327 Hoffman modulation jm 2010-03-09T03:20:14Z image FBbi:00000328 single sideband edge enhancement (SSBE) jm 2010-03-09T03:20:14Z image FBbi:00000329 interference reflection contrast (IRM) jm 2010-03-09T03:20:14Z image FBbi:00000330 interference contrast jm 2010-03-09T03:20:14Z image FBbi:00000331 polarization contrast jm 2010-03-09T03:24:02Z image FBbi:00000332 structured illumination microscopy (SIM) jm 2010-03-09T03:24:02Z image FBbi:00000333 point-localization method jm 2010-03-09T03:24:02Z image FBbi:00000334 stimulated emission depletion (STED) jm 2010-03-09T03:32:12Z image FBbi:00000335 PALM (photoactivation localization microscopy) jm 2010-03-09T03:32:12Z image FBbi:00000336 STORM (stochastic optical reconstruction microscopy) jm 2010-03-09T03:32:12Z image FBbi:00000337 FIONA (fluorescence imaging with one nanometer accuracy) jm 2010-03-09T03:32:12Z image FBbi:00000338 DOPI (defocussed orientation and position imaging) jm 2010-03-09T03:32:12Z image FBbi:00000339 PAINT (point accumulation for imaging in nanoscale topography) structured illumination used at sufficiently high power to cause significant ground-state depletion of the imaged fluorophore, thus allowing for non-linear resolution enhancement jm 2010-03-09T03:32:29Z image FBbi:00000340 saturated structured-illumination microscopy (SSIM) jm 2010-03-09T03:51:49Z image FBbi:00000341 UV/visible/IR illumination jm 2010-03-09T03:51:49Z image FBbi:00000342 X-ray illumination jm 2010-03-09T04:04:04Z image FBbi:00000343 microscopy with lenses imaging by means of a physical probe that passes over the sample jm 2010-03-09T04:04:04Z image FBbi:00000344 scanning probe microscopy jm 2010-03-09T04:18:03Z image mode of light microscopy FBbi:00000345 light microscopy jm 2010-03-09T10:19:35Z image FBbi:00000347 scanning tunneling microscopy jm 2010-03-09T10:19:35Z image FBbi:00000348 nearfield scanning optical microscopy (ANSOM) Aperture-less NSOM. jm 2010-03-09T10:20:01Z image FBbi:00000349 ANSOM jm 2010-03-09T10:23:41Z image FBbi:00000350 polarized light illumination jm 2010-03-09T10:25:08Z image FBbi:00000351 orientation-independent polarization microscopy jm 2010-03-09T10:27:11Z image FBbi:00000352 polarization-sensitive detection Uses an objective with extra components to manipulate the wave front in the plane of the objective aperture. jm 2010-03-09T10:41:27Z image FBbi:00000353 modified objective lens 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 linear computational contrast enhancing method method jm 2010-03-09T11:09:35Z image FBbi:00000354 linear method 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 non-linear computational contrast enhancing method method jm 2010-03-09T11:09:35Z image FBbi:00000355 non-linear method jm 2010-03-09T11:10:59Z image FBbi:00000356 Wiener filter jm 2010-03-09T11:10:59Z image FBbi:00000357 3D-deconvolution jm 2010-03-09T11:11:56Z image FBbi:00000358 no-neighbors deblurring jm 2010-03-09T11:11:56Z image FBbi:00000359 nearest-neighbors deblurring jm 2010-03-09T11:19:41Z image FBbi:00000360 constrained iterative deconvolution jm 2010-03-09T11:19:41Z image FBbi:00000361 maximum likelihood deconvolution jm 2010-03-09T11:19:41Z image FBbi:00000362 blind deconvolution jm 2010-03-09T11:19:42Z image FBbi:00000363 exhaustive photon reassignment illumination in the form of a thin sheet of light directed perpendicular to the optic axis jm 2010-03-11T10:06:20Z image FBbi:00000364 light-sheet illumination 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. jm 2010-03-11T10:09:33Z image FBbi:00000365 FLIP 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. jm 2010-03-11T10:09:33Z image FBbi:00000366 FRAP 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. XX:-new-dbxref- 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. jm 2010-03-11T10:09:33Z image FBbi:00000367 FRET jm 2010-03-11T10:09:33Z image FBbi:00000368 FLIM single (or selective) plane illumination. jm 2010-03-11T10:09:33Z image FBbi:00000369 SPIM coherent Raman anti-Stokes microscopy jm 2010-03-11T10:13:20Z image FBbi:00000370 CARS optical coherence tomography; an interferometric method of imaging using back-scattered photons (elastic scattering) jm 2010-03-11T10:32:19Z image FBbi:00000371 OCT image created using the electrons generated by ionization of a sample due to inelastic scattering of the primary beam of radiation jm 2010-03-12T08:34:44Z image FBbi:00000372 secondary_electron imaging imaged formed using electrons undergoing elastic scattering at very high angles, with emission of characteristic X-rays jm 2010-03-12T08:40:37Z image FBbi:00000373 back-scattered_electron imaging jm 2010-03-12T08:54:56Z image FBbi:00000374 detection of photons jm 2010-03-12T08:54:56Z image FBbi:00000375 detection of electrons jm 2010-03-12T08:54:56Z image FBbi:00000376 detection of acoustic waves jm 2010-03-12T08:54:56Z image FBbi:00000377 detection of current induced in the specimen jm 2010-03-12T08:55:29Z image FBbi:00000378 detection of UV/visible/IR photons jm 2010-03-12T08:55:29Z image FBbi:00000379 detection of X-ray photons jm 2010-03-12T09:12:36Z image FBbi:00000380 scanning-transmission electron microscopy jm 2010-03-12T09:16:40Z image EFTEM energy filtered TEM ESI electron spectroscopic imaging FBbi:00000381 EELS imaging jm 2010-03-12T09:16:40Z image FBbi:00000382 EDAX imaging 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 jm 2010-03-12T09:32:53Z image FBbi:00000383 specimen_modifying_illumination jm 2010-03-12T10:06:46Z image FBbi:00000384 photo-bleaching illumination jm 2010-03-12T10:06:46Z image FBbi:00000385 photo-ablation illumination jm 2010-03-12T10:06:46Z image FBbi:00000386 photo-switching illumination jm 2010-03-12T10:06:46Z image FBbi:00000387 photo-activation illumination jm 2010-03-12T10:06:46Z image FBbi:00000388 uncaging illumination jm 2010-03-12T10:06:46Z image FBbi:00000389 trapping illumination jm 2010-03-12T10:06:46Z image FBbi:00000390 emission-depletion illumination illumination in the shape of a thin line that is swept over the field of view jm 2010-03-12T10:31:26Z image FBbi:00000391 slit-scanning illumination illumination and detection via a thin slit jm 2010-03-12T10:32:36Z image FBbi:00000392 slit-scan confocal microscopy Fixed array of sources focused to an array of spots that is swept over the specimen in raster fashion jm 2010-03-12T10:35:43Z image FBbi:00000393 array-scan confocal microscopy jm 2010-03-12T10:39:24Z image FBbi:00000394 spot detector jm 2010-03-12T10:39:24Z image FBbi:00000395 area detector methods of visualization that differentiate between different regions or surfaces of the specimen based on contiguity jm 2010-03-14T08:38:50Z image FBbi:00000396 visualization of contiguous regions methods of visualization that differentiate regions of the specimen on the basis of their chemical properties jm 2010-03-14T08:38:50Z image FBbi:00000397 visualization by chemical attribute 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) jm 2010-03-14T08:44:06Z image FBbi:00000398 shadowing and plating visualization by exclusion of a stain in which the specimen is immersed; compare with "positive staining. jm 2010-03-14T08:44:06Z image FBbi:00000399 negative staining visualization of sequence-specific nucleic acid probe jm 2010-03-14T09:07:35Z image FBbi:00000400 sequence-specific nucleic acid probe visualization of antibody jm 2010-03-14T09:07:35Z image FBbi:00000401 antibody visualization of lectin jm 2010-03-14T09:07:35Z image FBbi:00000402 lectin visualization of small-molecule probe jm 2010-03-14T09:07:35Z image FBbi:00000403 small-molecule probe jm 2010-03-14T10:42:36Z image FBbi:00000404 fluorescent dextran fill visualization of fluorescent protein tag jm 2010-03-14T10:54:20Z image FBbi:00000405 fluorescent protein tag visualization of probes for nucleic acid jm 2010-03-14T09:25:57Z image FBbi:00000406 probes for nucleic acid visualization of small genetically encoded tag jm 2010-03-14T11:10:25Z image FBbi:00000407 small genetically encoded tag visualization of probe for protein jm 2010-03-14T09:25:57Z image FBbi:00000408 probe for protein visualization of organelle-specific probe jm 2010-03-14T09:25:57Z image FBbi:00000409 organelle-specific probe visualization of macromolecular probe jm 2010-03-14T09:26:11Z image FBbi:00000410 macromolecular probe visualization of probe for mitochondria jm 2010-03-14T09:28:19Z image FBbi:00000411 probe for mitochondria visualization of probe for endoplasmic reticulum jm 2010-03-14T09:28:19Z image FBbi:00000412 probe for endoplasmic reticulum visualization of probe for Golgi jm 2010-03-14T09:28:19Z image FBbi:00000413 probe for Golgi visualization of probe for lysosomes jm 2010-03-14T09:28:19Z image FBbi:00000414 probe for lysosomes visualization of stain with broad specificity jm 2010-03-15T11:51:34Z image positive staining FBbi:00000415 stain with broad specificity visualization of tetracysteine tag jm 2010-03-14T11:12:03Z image FBbi:00000416 tetracysteine tag visualization of Hoechst 33258 jm 2010-03-14T09:33:18Z image FBbi:00000417 Hoechst 33258 visualization of genetically encoded biotin tag jm 2010-03-14T11:12:03Z image FBbi:00000418 genetically encoded biotin tag jm 2010-03-17T01:55:02Z image FBbi:00000419 freeze_fracture/freeze_etch visualization of fluorescent protein derived from Aequorea victoria jm 2010-03-17T01:59:59Z image FBbi:00000420 fluorescent protein derived from Aequorea victoria visualization of membrane-permeant probe jm 2010-03-14T09:33:53Z image FBbi:00000421 membrane-permeant probe visualization of membrane impermeant probe jm 2010-03-14T09:33:53Z image FBbi:00000422 membrane impermeant probe visualization of acridine homodimer jm 2010-03-14T09:42:34Z image FBbi:00000423 acridine homodimer visualization of 7-amino-actinomycin D jm 2010-03-14T09:42:34Z image FBbi:00000424 7-amino-actinomycin D visualization of conconavalin A jm 2010-03-14T09:48:57Z image FBbi:00000425 conconavalin A visualization of wheat germ agglutinin jm 2010-03-14T09:48:57Z image FBbi:00000426 wheat germ agglutinin visualization of Phaseolus vulgaris lectin PHA-L) jm 2010-03-14T09:48:57Z image FBbi:00000427 Phaseolus vulgaris lectin PHA-L) visualization of Arachis hypogaea (PNA) jm 2010-03-14T09:48:57Z image FBbi:00000428 Arachis hypogaea (PNA) visualization of Helix pomatia agglutinin jm 2010-03-14T09:48:57Z image FBbi:00000429 Helix pomatia agglutinin visualization of soybean agglutinin jm 2010-03-14T09:48:57Z image FBbi:00000430 soybean agglutinin visualization of cholera toxin B jm 2010-03-14T09:48:57Z image FBbi:00000431 cholera toxin B visualization of peptide-nucleic acid probe jm 2010-03-14T09:52:30Z image FBbi:00000432 peptide-nucleic acid probe visualization of fluorescent protein derived from Anthozoa jm 2010-03-17T01:59:59Z image FBbi:00000433 fluorescent protein derived from Anthozoa visualization of optical highlighter jm 2010-03-17T01:59:59Z image FBbi:00000434 optical highlighter visualization of Blue fluorescent protein from Aequorea victoria jm 2010-03-17T02:01:22Z image FBbi:00000435 Blue fluorescent protein from Aequorea victoria visualization of Cyan fluorescent protein from Aequorea jm 2010-03-17T02:01:22Z image FBbi:00000436 Cyan fluorescent protein from Aequorea visualization of Green fluorescent protein from Aequorea jm 2010-03-17T02:01:22Z image FBbi:00000437 Green fluorescent protein from Aequorea visualization of DiIC16 jm 2010-03-14T10:15:00Z image FBbi:00000438 DiIC16 visualization of Yellow fluorescent protein from Aequorea jm 2010-03-17T02:01:22Z image FBbi:00000439 Yellow fluorescent protein from Aequorea visualization of Alexa Fluor 488 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000440 Alexa Fluor 488 visualization of Alexa Fluor 546 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000441 Alexa Fluor 546 visualization of Alexa Fluor 568 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000442 Alexa Fluor 568 visualization of Alexa Fluor 555 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000443 Alexa Fluor 555 visualization of Alexa Fluor 594 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000444 Alexa Fluor 594 visualization of Alexa Fluor 610 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000445 Alexa Fluor 610 visualization of Alexa Fluor 633 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000446 Alexa Fluor 633 visualization of Alexa Fluor 647 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000447 Alexa Fluor 647 visualization of Cy2 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000448 Cy2 visualization of Cy3 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000449 Cy3 visualization of Cy5 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000450 Cy5 visualization of Fluorescein (FITC) conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000451 Fluorescein (FITC) visualization of Rhodamine conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000452 Rhodamine fluorophore with ex/em 589/615 visualization of TexasRed conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000453 TexasRed fluorophore derivative of rhodamine with ex/em 547/572 visualization of Tetramethyl rhodamine (TRITC) conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000454 Tetramethyl rhodamine (TRITC) visualization of fluorescent label conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000455 fluorescent label visualization of enzyme label conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000456 enzyme label visualization of electron dense label conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000457 electron dense label visualization of biotin conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000458 biotin visualization of affinity for specific proteins jm 2010-03-14T10:28:34Z image FBbi:00000459 affinity for specific proteins visualization of non-specific protein affinity jm 2010-03-14T10:28:34Z image FBbi:00000460 non-specific protein affinity visualization of AzuriteFP jm 2010-03-17T02:09:45Z image FBbi:00000461 AzuriteFP visualization of SiriusFP jm 2010-03-17T02:09:45Z image FBbi:00000462 SiriusFP visualization of non-immunological protein probe jm 2010-03-14T10:32:01Z image FBbi:00000463 non-immunological protein probe visualization of alpha-bungarotoxin jm 2010-03-14T10:36:52Z image FBbi:00000464 alpha-bungarotoxin visualization of botulinum toxin jm 2010-03-14T10:36:52Z image FBbi:00000465 botulinum toxin visualization of tetrodotoxin jm 2010-03-14T10:37:23Z image FBbi:00000466 tetrodotoxin visualization of batrachatoxin jm 2010-03-14T10:37:23Z image FBbi:00000467 batrachatoxin visualization of CeruleanFP jm 2010-03-17T02:10:21Z image FBbi:00000468 CeruleanFP visualization of CyPet jm 2010-03-17T02:10:21Z image FBbi:00000469 CyPet visualization of SCFP jm 2010-03-17T02:10:21Z image FBbi:00000470 SCFP visualization of EmeraldFP jm 2010-03-17T02:11:07Z image FBbi:00000471 EmeraldFP visualization of SuperfolderFP jm 2010-03-17T02:11:07Z image FBbi:00000472 SuperfolderFP visualization of T-SapphireFP jm 2010-03-17T02:11:07Z image FBbi:00000473 T-SapphireFP visualization of CitrineFP jm 2010-03-17T02:14:30Z image FBbi:00000474 CitrineFP visualization of SYFP jm 2010-03-17T02:14:30Z image FBbi:00000475 SYFP visualization of TopazFP jm 2010-03-17T02:14:30Z image FBbi:00000476 TopazFP visualization of VenusFP jm 2010-03-17T02:14:30Z image FBbi:00000477 VenusFP visualization of yPet jm 2010-03-17T02:14:30Z image FBbi:00000478 yPet visualization of Blue fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000479 Blue fluorescent proteins from Anthozoa visualization of Cyan fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000480 Cyan fluorescent proteins from Anthozoa visualization of Green fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000481 Green fluorescent proteins from Anthozoa visualization of Orange fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000482 Orange fluorescent proteins from Anthozoa visualization of Red fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000483 Red fluorescent proteins from Anthozoa visualization of Far-red fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000484 Far-red fluorescent proteins from Anthozoa visualization of Yellow fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000485 Yellow fluorescent proteins from Anthozoa visualization of mTagBFP jm 2010-03-17T02:16:38Z image FBbi:00000486 mTagBFP visualization of AmCyanFP jm 2010-03-17T02:17:42Z image FBbi:00000487 AmCyanFP visualization of mCyFP jm 2010-03-17T02:17:42Z image FBbi:00000488 mCyFP visualization of mTFP1 jm 2010-03-17T02:17:42Z image FBbi:00000489 mTFP1 visualization of TagCFP jm 2010-03-17T02:17:42Z image FBbi:00000490 TagCFP visualization of AQ143 jm 2010-03-17T02:19:04Z image FBbi:00000491 AQ143 visualization of HcRed-tandemFP jm 2010-03-17T02:19:04Z image FBbi:00000492 HcRed-tandemFP visualization of KatushkaFP jm 2010-03-17T02:19:04Z image FBbi:00000493 KatushkaFP visualization of mKateFP jm 2010-03-17T02:19:04Z image FBbi:00000494 mKateFP visualization of mKate2FP jm 2010-03-17T02:19:04Z image FBbi:00000495 mKate2FP visualization of mPlumFP jm 2010-03-17T02:19:04Z image FBbi:00000496 mPlumFP visualization of tdKatuskaFP jm 2010-03-17T02:19:04Z image FBbi:00000497 tdKatuskaFP visualization of tdRFP639 jm 2010-03-17T02:19:04Z image FBbi:00000498 tdRFP639 visualization of AceFP jm 2010-03-17T02:20:00Z image FBbi:00000499 AceFP visualization of Azami GreenFP jm 2010-03-17T02:20:00Z image FBbi:00000500 Azami GreenFP visualization of CopGFP jm 2010-03-17T02:20:00Z image FBbi:00000501 CopGFP visualization of mWasabiFP jm 2010-03-17T02:20:00Z image FBbi:00000502 mWasabiFP visualization of TagGFP jm 2010-03-17T02:20:00Z image FBbi:00000503 TagGFP visualization of TagGFP2 jm 2010-03-17T02:20:00Z image FBbi:00000504 TagGFP2 visualization of ZsGreenFP jm 2010-03-17T02:20:00Z image FBbi:00000505 ZsGreenFP visualization of DsRed-ExpressFP jm 2010-03-17T02:22:53Z image FBbi:00000506 DsRed-ExpressFP visualization of DsRed-Express2FP jm 2010-03-17T02:22:53Z image FBbi:00000507 DsRed-Express2FP visualization of DsRed-MaxFP jm 2010-03-17T02:22:53Z image FBbi:00000508 DsRed-MaxFP visualization of DsRed-monomerFP jm 2010-03-17T02:22:53Z image FBbi:00000509 DsRed-monomerFP visualization of DsRed2FP jm 2010-03-17T02:22:53Z image FBbi:00000510 DsRed2FP visualization of dTomatoFP jm 2010-03-17T02:22:53Z image FBbi:00000511 dTomatoFP visualization of Kusabira OrangeFP jm 2010-03-17T02:22:53Z image FBbi:00000512 Kusabira OrangeFP visualization of Kusabira OrangeFP2 jm 2010-03-17T02:22:53Z image FBbi:00000513 Kusabira OrangeFP2 visualization of mOrangeFP jm 2010-03-17T02:22:53Z image FBbi:00000514 mOrangeFP visualization of mOrange2FP jm 2010-03-17T02:22:53Z image FBbi:00000515 mOrange2FP visualization of TagRFP jm 2010-03-17T02:22:53Z image FBbi:00000516 TagRFP visualization of TagRFP-T jm 2010-03-17T02:22:53Z image FBbi:00000517 TagRFP-T visualization of tdTomatoFP jm 2010-03-17T02:22:53Z image FBbi:00000518 tdTomatoFP visualization of turboRFP jm 2010-03-17T02:22:53Z image FBbi:00000519 turboRFP visualization of AsRed2FP jm 2010-03-17T02:24:26Z image FBbi:00000520 AsRed2FP visualization of eqFP611 jm 2010-03-17T02:24:26Z image FBbi:00000521 eqFP611 visualization of HcRed1FP jm 2010-03-17T02:24:26Z image FBbi:00000522 HcRed1FP visualization of JRedFP jm 2010-03-17T02:24:26Z image FBbi:00000523 JRedFP visualization of mAppleFP jm 2010-03-17T02:24:26Z image FBbi:00000524 mAppleFP visualization of mCherryFP jm 2010-03-17T02:24:26Z image FBbi:00000525 mCherryFP visualization of mRasberryFP jm 2010-03-17T02:24:26Z image FBbi:00000526 mRasberryFP visualization of mRFP1 jm 2010-03-17T02:24:26Z image FBbi:00000527 mRFP1 visualization of mRubyFP jm 2010-03-17T02:24:26Z image FBbi:00000528 mRubyFP visualization of mStrawberryFP jm 2010-03-17T02:24:26Z image FBbi:00000529 mStrawberryFP visualization of tdRFP611 jm 2010-03-17T02:24:26Z image FBbi:00000530 tdRFP611 visualization of PhiYFP jm 2010-03-17T02:25:15Z image FBbi:00000531 PhiYFP visualization of TagYFP jm 2010-03-17T02:25:15Z image FBbi:00000532 TagYFP visualization of TurboYFP jm 2010-03-17T02:25:15Z image FBbi:00000533 TurboYFP visualization of ZsYellowFP jm 2010-03-17T02:25:15Z image FBbi:00000534 ZsYellowFP visualization of fluorescent protein timer jm 2010-03-17T02:27:50Z image FBbi:00000535 fluorescent protein timer visualization of photoactivatable fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000536 photoactivatable fluorescent protein visualization of photoconvertible fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000537 photoconvertible fluorescent protein visualization of photoconvertible/photoswitchable fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000538 photoconvertible/photoswitchable fluorescent protein visualization of photoswitchable fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000539 photoswitchable fluorescent protein visualization of DsRed-ES FP jm 2010-03-17T02:29:47Z image FBbi:00000540 DsRed-ES FP visualization of Fast-FT jm 2010-03-17T02:29:47Z image FBbi:00000541 Fast-FT visualization of Medium-FT jm 2010-03-17T02:29:47Z image FBbi:00000542 Medium-FT visualization of Slow-FT jm 2010-03-17T02:29:47Z image FBbi:00000543 Slow-FT visualization of PA-GFP jm 2010-03-17T02:31:26Z image FBbi:00000544 PA-GFP visualization of PA-CFP jm 2010-03-17T02:31:26Z image FBbi:00000545 PA-CFP visualization of PA-mCherry1FP jm 2010-03-17T02:31:26Z image FBbi:00000546 PA-mCherry1FP visualization of PA-mRFP jm 2010-03-17T02:31:26Z image FBbi:00000547 PA-mRFP visualization of Phamret jm 2010-03-17T02:31:26Z image FBbi:00000548 Phamret visualization of Dendra2FP jm 2010-03-17T02:32:35Z image FBbi:00000549 Dendra2FP visualization of dEOSFP jm 2010-03-17T02:32:35Z image FBbi:00000550 dEOSFP visualization of KaedeFP jm 2010-03-17T02:32:35Z image FBbi:00000551 KaedeFP visualization of mEOS2FP jm 2010-03-17T02:32:35Z image FBbi:00000552 mEOS2FP visualization of mKikGR jm 2010-03-17T02:32:35Z image FBbi:00000553 mKikGR visualization of wtEOSFP jm 2010-03-17T02:32:35Z image FBbi:00000554 wtEOSFP visualization of wtKIikGR jm 2010-03-17T02:32:35Z image FBbi:00000555 wtKIikGR visualization of IrisFP jm 2010-03-17T02:32:44Z image FBbi:00000556 IrisFP visualization of bsDronpa jm 2010-03-17T02:34:12Z image FBbi:00000557 bsDronpa visualization of Dronpa jm 2010-03-17T02:34:12Z image FBbi:00000558 Dronpa visualization of Dronpa-3 jm 2010-03-17T02:34:12Z image FBbi:00000559 Dronpa-3 visualization of E2GFP jm 2010-03-17T02:34:12Z image FBbi:00000560 E2GFP visualization of KFP1 jm 2010-03-17T02:34:12Z image FBbi:00000561 KFP1 visualization of mTFP0.7 jm 2010-03-17T02:34:12Z image FBbi:00000562 mTFP0.7 visualization of PadronFP jm 2010-03-17T02:34:12Z image FBbi:00000563 PadronFP visualization of rsCherryFP jm 2010-03-17T02:34:12Z image FBbi:00000564 rsCherryFP visualization of rsCherryRevFP jm 2010-03-17T02:34:12Z image FBbi:00000565 rsCherryRevFP visualization of rsFastLimeFP jm 2010-03-17T02:34:12Z image FBbi:00000566 rsFastLimeFP visualization of optically-dense stain jm 2010-04-27T10:29:56Z image FBbi:00000567 optically-dense stain visualization of electron-dense stain jm 2010-04-27T10:29:56Z image FBbi:00000568 electron-dense stain visualization of uranyl salt jm 2010-04-27T10:38:31Z image FBbi:00000569 uranyl salt visualization of lead salt jm 2010-04-27T10:38:31Z image FBbi:00000570 lead salt visualization of osmium tetroxide jm 2010-04-27T10:38:31Z image FBbi:00000571 osmium tetroxide visualization of potassium permanganate jm 2010-04-27T10:38:31Z image FBbi:00000572 potassium permanganate jm 2010-04-27T10:39:43Z image FBbi:00000573 uranium compound jm 2010-04-27T10:39:43Z image FBbi:00000574 molybdenum compound jm 2010-04-27T10:39:43Z image FBbi:00000575 tungsten compound jm 2010-04-27T10:39:43Z image FBbi:00000576 aurothioglucose jm 2010-04-28T06:06:52Z image FBbi:00000577 other negative stain visualization of metabolically incorporated other radioisotope jm 2010-04-28T06:08:02Z image FBbi:00000578 other radioisotope A fragment of a cell, subcellular organelle, or macromolecular complex. jm 2010-04-28T06:08:42Z image FBbi:00000579 isolated subcellular component electrons generated by inelastic scattering of other radiation, the primary radiation. jm 2010-05-04T12:25:14Z image FBbi:00000580 secondary electron generation specimen from which water has been removed by a process that avoids liquid-gas and solid-gas phase transitions. jm 2010-05-04T12:31:12Z image FBbi:00000581 critical_point dried specimen data as acquired, with no alterations that change the pixel values. jm 2010-05-04T12:42:17Z image FBbi:00000582 unprocessed raw data specimen from which water has been removed by evaporation under vacuum at a temperature below freezing. jm 2010-05-04T12:49:31Z image FBbi:00000583 lyophilized specimen fluorophore derivative of rhodamine with ex/em 580/605 visualization of X-Rhodamine conjugated to probe jm 2010-05-04T09:02:54Z image FBbi:00000584 X-Rhodamine A method of reconstructing 3D structure by combining serial sectioning with scanning EM. jm 2010-09-02T05:10:33Z image FBbi:00000585 serial block face SEM (SBFSEM) A method of reconstructing 3D structure by combining serial sectioning with scanning EM. PMID:15514700 jm 2010-09-03T08:42:47Z image FBbi:00000586 elastic scattering of electrons jm 2010-09-03T08:42:47Z image FBbi:00000587 elastic scattering of photons jm 2010-09-03T08:43:42Z image FBbi:00000588 inelastic scattering of electrons jm 2010-09-03T08:43:42Z image FBbi:00000589 inelastic scattering of photons (Raman scattering) The source of the variation in the imaged parameter across the field of view. jm 2010-09-03T08:53:13Z image FBbi:00000590 source of contrast jm 2010-09-03T09:55:12Z image FBbi:00000591 differences in chemical composition jm 2010-09-03T09:55:12Z image FBbi:00000592 distribution of epitope jm 2010-09-03T09:55:12Z image FBbi:00000593 form birefringence jm 2010-09-03T09:55:12Z image FBbi:00000594 intrinsic birefringence jm 2010-09-03T09:55:12Z image FBbi:00000595 stress-induced birefringence jm 2010-09-03T09:55:12Z image FBbi:00000596 distribution of a specific nucleic acid sequence jm 2010-09-03T09:55:12Z image FBbi:00000597 distribution of a specific protein jm 2010-09-03T09:55:12Z image FBbi:00000598 differences in adsorption or binding of stain jm 2010-09-03T09:55:12Z image FBbi:00000599 boundaries between regions with different refractive index jm 2010-09-03T09:55:12Z image FBbi:00000600 differences in amount of elastic light scattering jm 2010-09-04T11:57:06Z image FBbi:00000601 differences in deposition of metal shadow jm 2010-09-04T12:55:54Z image FBbi:00000602 differences in intrinsic optical density jm 2010-09-04T01:28:20Z image FBbi:00000603 fluorescence polarization microscopy jm 2010-09-04T01:31:54Z image FBbi:00000604 compartmentalization of stain or label jm 2010-09-04T01:35:37Z image FBbi:00000605 differences in fluorescence lifetime jm 2010-09-04T01:36:45Z image FBbi:00000606 differences in orientation of fluorophore jm 2010-09-04T01:51:14Z image FBbi:00000607 intrinsic mass distribution jm 2010-09-04T02:05:02Z image FBbi:00000608 X-ray fluorescence jm 2010-09-04T11:49:25Z image FBbi:00000609 heat fixed tissue visualization of copper salt jm 2010-09-04T11:56:02Z image FBbi:00000610 copper salt jm 2010-09-28T04:35:54Z image FBbi:00000611 dispersed cells in vitro visualization of fluorescent protein derived from Arabidopsis jm 2011-05-23T09:33:44Z image FBbi:00000612 fluorescent protein derived from Arabidopsis jm 2011-05-23T09:49:58Z image FBbi:00000613 vidicon tube camera visualization of phototropin 2 jm 2011-05-23T09:55:54Z image FBbi:00000614 phototropin 2 visualization of miniSOG jm 2011-05-23T09:57:01Z image FBbi:00000615 miniSOG jm 2011-05-23T10:09:41Z image FTIR frustrated total internal reflection FBbi:00000616 evanescent wave scattering jm 2011-05-23T10:10:58Z image total internal reflection fluorescence TIRF FBbi:00000617 evanescent wave microscopy jm 2011-05-23T10:34:07Z image FBbi:00000618 ground state depletion scanning (GSD) jm 2011-05-23T10:43:15Z image FBbi:00000619 nearfield illumination jm 2011-05-23T10:44:03Z image FBbi:00000620 nearfield illumination jm 2011-05-23T10:51:16Z image FBbi:00000621 freeze-substituted tissue jm 2011-05-23T10:53:45Z image FBbi:00000622 high-voltage electron microscopy (HVEM) jm 2011-05-23T10:53:45Z image FBbi:00000623 intermediate voltage electron microacopy (IVEM) An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination. image FBbi:00001000 radiography An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination. http://en.wikipedia.org/w/index.php?title=Radiography&oldid=606628211 Radiography using X-rays X-radiography image X-ray FBbi:00001001 X-ray radiography MeSH:D014057 http://en.wikipedia.org/wiki/X-ray_computed_tomography CAT scan CT scan X-ray CT image computed axial tomography FBbi:00001002 X-ray computed tomography Tomography using X-ray illumination. image FBbi:00001003 X-ray tomography An imaging technique that creates virtual sections through the use of any kind of penetrating wave. image FBbi:00001004 tomography 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. image FBbi:00001005 computed tomography image FBbi:00001006 x-ray/gamma ray illumination image FBbi:00001007 gamma ray illumination image FBbi:00001012 fixation method 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. FIB-SEM image FBbi:00050000 focussed ion beam scanning electron microscopy (FIB-SEM) 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. PMID:22119321 image FBbi_root:00000000 method involved in biological imaging molecular process molecular_function catalytic activity biological_process true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups true 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 infer input from direct reg 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' enabling an MF enables its parts true 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' involved in BP 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" 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. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).