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 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 BFO:0000002 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 BFO:0000003 An entity that has temporal parts and that happens, unfolds or develops through time. occurrent BFO:0000004 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 BFO:0000015 An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process BFO:0000040 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity CARO:0000000 anatomical entity CARO:0030000 biological entity jm 2010-03-07T02:05:26Z image FBbi:00000000 dummy term true FBbi:00000000 image FBbi:00000001 sample preparation method FBbi:00000001 image FBbi:00000002 chemically fixed tissue FBbi:00000002 image FBbi:00000003 coagulating-fixative fixed tissue FBbi:00000003 image FBbi:00000004 acetone fixed tissue FBbi:00000004 image FBbi:00000005 acrolein fixed tissue FBbi:00000005 image FBbi:00000006 ethanol fixed tissue FBbi:00000006 image FBbi:00000007 methanol fixed tissue FBbi:00000007 image FBbi:00000008 crosslinking-fixative fixed tissue FBbi:00000008 image EGS FBbi:00000009 ethylene glycol-bis-succinimidyl succinate fixed tissue FBbi:00000009 image FBbi:00000010 formaldehyde fixed tissue FBbi:00000010 image FBbi:00000011 glutaraldehyde fixed tissue FBbi:00000011 image FBbi:00000012 osmium tetroxide fixed tissue FBbi:00000012 image FBbi:00000013 cryofixed tissue FBbi:00000013 image FBbi:00000014 unfixed tissue FBbi:00000014 image FBbi:00000015 embedded tissue FBbi:00000015 image FBbi:00000016 tissue in plastic embedment FBbi:00000016 image FBbi:00000017 tissue in acrylic resin embedment FBbi:00000017 image FBbi:00000018 tissue in epoxy resin embedment FBbi:00000018 image FBbi:00000019 tissue in wax embedment FBbi:00000019 image FBbi:00000020 tissue in paraffin embedment FBbi:00000020 image FBbi:00000021 tissue in polyester wax embedment FBbi:00000021 image FBbi:00000022 tissue in polyethylene glycol embedment FBbi:00000022 image FBbi:00000023 unembedded tissue FBbi:00000023 image FBbi:00000024 whole mounted tissue FBbi:00000024 Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state. image live-cell imaging FBbi:00000025 living tissue FBbi:00000025 Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state. XX:ISBN978-087969683-2 image FBbi:00000026 sectioned tissue FBbi:00000026 image FBbi:00000027 cryostat-sectioned tissue FBbi:00000027 image FBbi:00000028 hand-sectioned tissue FBbi:00000028 image FBbi:00000029 microtome-sectioned tissue FBbi:00000029 image FBbi:00000030 vibratome-sectioned tissue FBbi:00000030 image FBbi:00000031 visualization method FBbi:00000031 image FBbi:00000032 endogenous substrate, non-vital dye true FBbi:00000032 image FBbi:00000033 diagram FBbi:00000033 visualization of HA peptide tag image FBbi:00000034 HA peptide tag FBbi:00000034 visualization of cresyl fast violet image FBbi:00000035 cresyl fast violet FBbi:00000035 image FBbi:00000036 endogenous substrate, diaminobenzidine true FBbi:00000036 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 FBbi:00000037 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 FBbi:00000038 visualization of fuchsin image FBbi:00000039 fuchsin FBbi:00000039 visualization of giemsa image FBbi:00000040 giemsa FBbi:00000040 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 FBbi:00000041 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 FBbi:00000042 visualization of methyl violet image FBbi:00000043 methyl violet FBbi:00000043 visualization of nitro blue tetrazolium chloride image FBbi:00000044 nitro blue tetrazolium chloride FBbi:00000044 visualization of nuclear fast red image FBbi:00000045 nuclear fast red FBbi:00000045 visualization of orcein image FBbi:00000046 orcein FBbi:00000046 visualization of propidium iodide image PI FBbi:00000047 propidium iodide FBbi:00000047 visualization of SYTOX Green image FBbi:00000048 SYTOX Green FBbi:00000048 visualization of toluidine blue image FBbi:00000049 toluidine blue FBbi:00000049 image FBbi:00000050 endogenous substrate, vital dye true FBbi:00000050 visualization of acridine orange image AO FBbi:00000051 acridine orange FBbi:00000051 visualization of Hoechst 33342 image HO342 Hoechst 33342 FBbi:00000052 Hoechst 33342 FBbi:00000052 visualization of cationic colloidal gold image FBbi:00000053 cationic colloidal gold FBbi:00000053 visualization of CMX rosamine (Mitotracker Red) image Mitotracker X FBbi:00000054 CMX rosamine (Mitotracker Red) FBbi:00000054 visualization of DiOC6 (3,3'-dihexyloxacarbocyanine iodide) image DiOC FBbi:00000055 DiOC6 (3,3'-dihexyloxacarbocyanine iodide) FBbi:00000055 visualization of 4',6-diamidino-2-phenylindole (DAPI) image DAPI FBbi:00000056 4',6-diamidino-2-phenylindole (DAPI) FBbi:00000056 image FBbi:00000057 lucifer yellow FBbi:00000057 visualization of methylene blue image FBbi:00000058 methylene blue FBbi:00000058 visualization of Nile blue A image FBbi:00000059 Nile blue A FBbi:00000059 visualization of Nile red image FBbi:00000060 Nile red FBbi:00000060 visualization of pyronine image FBbi:00000061 pyronine FBbi:00000061 visualization of rhodamine 123 image FBbi:00000062 rhodamine 123 FBbi:00000062 visualization of rhodamine B image FBbi:00000063 rhodamine B FBbi:00000063 visualization of SYTO Blue image FBbi:00000064 SYTO Blue FBbi:00000064 visualization of SYTO Green image FBbi:00000065 SYTO Green FBbi:00000065 visualization of SYTO Orange image FBbi:00000066 SYTO Orange FBbi:00000066 visualization of SYTO Red image FBbi:00000067 SYTO Red FBbi:00000067 visualization of YO-PRO-1 image FBbi:00000068 YO-PRO-1 FBbi:00000068 image FBbi:00000069 endogenous substrate, dye conjugate true FBbi:00000069 image LysoTracker FBbi:00000070 endogenous substrate, acidotropic-fluor conjugate true FBbi:00000070 image FBbi:00000071 endogenous substrate, lectin-fluor conjugate true FBbi:00000071 image FBbi:00000072 endogenous substrate, lectin-gold conjugate true FBbi:00000072 visualization of taxol image FBbi:00000073 taxol FBbi:00000073 image FBbi:00000074 endogenous substrate, phalloidin-fluor conjugate true FBbi:00000074 image FBbi:00000075 exogenous label true FBbi:00000075 visualization of genetically encoded enzyme image FBbi:00000076 genetically encoded enzyme FBbi:00000076 visualization of beta-galactosidase image lacZ, X-gal FBbi:00000077 beta-galactosidase FBbi:00000077 visualization of beta-glucuronidase image GUS, X-gluc FBbi:00000078 beta-glucuronidase FBbi:00000078 visualization of genetically encoded tag image FBbi:00000079 genetically encoded tag FBbi:00000079 visualization of EBFP image BFP FBbi:00000080 EBFP FBbi:00000080 visualization of ECFP image CFP FBbi:00000081 ECFP FBbi:00000081 visualization of EGFP image GFP FBbi:00000082 EGFP FBbi:00000082 image RFP FBbi:00000083 Aequorea victoria red fluorescent protein tag true FBbi:00000083 visualization of EYFP image YFP FBbi:00000084 EYFP FBbi:00000084 visualization of DsRed image DsRed FBbi:00000085 DsRed FBbi:00000085 visualization of c-MYC peptide tag image FBbi:00000086 c-MYC peptide tag FBbi:00000086 visualization of FLAG peptide tag image FBbi:00000087 FLAG peptide tag FBbi:00000087 visualization of the connected regions of a cell by filling with a label image FBbi:00000088 intracellular filling FBbi:00000088 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 FBbi:00000089 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 FBbi:00000090 image FBbi:00000091 5-SFX fluorescein RNA fill FBbi:00000091 image FBbi:00000092 X-rhodamine RNA fill FBbi:00000092 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 FBbi:00000093 image FBbi:00000094 fluor labeled protein fill FBbi:00000094 image FBbi:00000095 fluor conjugated actin fill FBbi:00000095 image FBbi:00000096 Alexa Fluor 488 actin fill true FBbi:00000096 image FBbi:00000097 Alexa Fluor 568 actin fill true FBbi:00000097 image FBbi:00000098 fluoresceine actin fill true FBbi:00000098 image FBbi:00000099 rhodamine actin fill true FBbi:00000099 visualization of phalloidin image FBbi:00000100 phalloidin FBbi:00000100 image FBbi:00000101 Alexa Fluor 350 phalloidin fill true FBbi:00000101 image FBbi:00000102 Alexa Fluor 488 phalloidin fill true FBbi:00000102 image FBbi:00000103 eosin phalloidin fill true FBbi:00000103 image FBbi:00000104 fluoresceine phalloidin fill true FBbi:00000104 image FBbi:00000105 Oregon Green 488 phalloidin fill true FBbi:00000105 image FBbi:00000106 Oregon Green 514 phalloidin fill true FBbi:00000106 image FBbi:00000107 rhodamine phalloidin fill true FBbi:00000107 image FBbi:00000108 Texas Red-X phalloidin fill true FBbi:00000108 image FBbi:00000109 fluor conjugated tubulin fill FBbi:00000109 image FBbi:00000110 Oregon Green 514 tubulin fill true FBbi:00000110 image FBbi:00000111 X-rhodamine tubulin fill true FBbi:00000111 visualization of probe for lipid image FBbi:00000112 probe for lipid FBbi:00000112 visualization of DiA image FBbi:00000113 DiA FBbi:00000113 visualization of DiD image FBbi:00000114 DiD FBbi:00000114 visualization of DiI image FBbi:00000115 DiI FBbi:00000115 visualization of DiO image FBbi:00000116 DiO FBbi:00000116 visualization of DiR image FBbi:00000117 DiR FBbi:00000117 image FBbi:00000118 miscellaneous fill FBbi:00000118 image Neurobiotin FBbi:00000119 biotin ethylenediamine fill FBbi:00000119 image FBbi:00000120 cobalt fill FBbi:00000120 image FBbi:00000121 silver-intensified cobalt fill FBbi:00000121 visualization of metabolically incorporated radioisotope image FBbi:00000122 metabolically incorporated radioisotope FBbi:00000122 visualization of metabolically incorporated [14]C image FBbi:00000123 [14]C FBbi:00000123 visualization of metabolically incorporated [32]P image FBbi:00000124 [32]P FBbi:00000124 visualization of metabolically incorporated [33]P image FBbi:00000125 [33]P FBbi:00000125 visualization of metabolically incorporated [35]S image FBbi:00000126 [35]S FBbi:00000126 visualization of metabolically incorporated [3]H image FBbi:00000127 [3]H FBbi:00000127 image FBbi:00000128 vizualization of label conjugated to probe FBbi:00000128 tissue made permeable by the action of glycerol jm 2010-03-07T02:37:12Z image glycerinated tissue FBbi:00000129 glycerol permeabilized FBbi:00000129 visualization of labeled primary antibody image FBbi:00000130 labeled primary antibody FBbi:00000130 image FBbi:00000131 primary antibody-enzyme conjugate, substrate true FBbi:00000131 visualization of alkaline phosphatase conjugated to probe image FBbi:00000132 alkaline phosphatase FBbi:00000132 image FBbi:00000133 primary antibody-alkaline phosphastase conjugate, DAB true FBbi:00000133 image FBbi:00000134 primary antibody-alkaline phosphastase conjugate, ELF 97 phosphate true FBbi:00000134 image FBbi:00000135 primary antibody-alkaline phosphastase conjugate, Vector Black true FBbi:00000135 image FBbi:00000136 primary antibody-alkaline phosphastase conjugate, Vector Blue true FBbi:00000136 image FBbi:00000137 primary antibody-alkaline phosphastase conjugate, Vector Red true FBbi:00000137 visualization of horseradish peroxidase conjugated to probe image FBbi:00000138 horseradish peroxidase FBbi:00000138 image FBbi:00000139 primary antibody-horseradish peroxidase, 4-chloro-1-naphthol true FBbi:00000139 image FBbi:00000140 primary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole true FBbi:00000140 image FBbi:00000141 primary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine true FBbi:00000141 image FBbi:00000142 primary antibody-horseradish peroxidase, Vector NovaRed true FBbi:00000142 image FBbi:00000143 primary antibody-horseradish peroxidase, Vector SG true FBbi:00000143 image FBbi:00000144 primary antibody-horseradish peroxidase, Vector VIP true FBbi:00000144 image FBbi:00000145 primary antibody-fluor conjugate true FBbi:00000145 image AMCA FBbi:00000146 primary antibody-aminomethylcoumarin acetate true FBbi:00000146 image FBbi:00000147 primary antibody-Cascade blue true FBbi:00000147 image Cy2 FBbi:00000148 primary antibody-cyanine true FBbi:00000148 image FITC FBbi:00000149 primary antibody-fluorescein isothiocyanate true FBbi:00000149 image Cy3 FBbi:00000150 primary antibody-indocarbocyanine true FBbi:00000150 image Cy5 FBbi:00000151 primary antibody-indodicarbocyanine true FBbi:00000151 image RRX FBbi:00000152 primary antibody-rhodamine red-X true FBbi:00000152 image TRITC FBbi:00000153 primary antibody-tetramethyl rhodamine isothiocyanate true FBbi:00000153 image TR FBbi:00000154 primary antibody-Texas Red true FBbi:00000154 image FBbi:00000155 primary antibody-gold conjugate true FBbi:00000155 visualization of primary antibody plus labeled secondary antibody image FBbi:00000156 primary antibody plus labeled secondary antibody FBbi:00000156 image FBbi:00000157 secondary antibody-enzyme conjugate, substrate true FBbi:00000157 visualization of acid phosphatase conjugated to probe image FBbi:00000158 acid phosphatase FBbi:00000158 image FBbi:00000159 secondary antibody-alkaline phosphastase conjugate, DAB true FBbi:00000159 image FBbi:00000160 secondary antibody-alkaline phosphastase conjugate, ELF 97 phosphate true FBbi:00000160 image FBbi:00000161 secondary antibody-alkaline phosphastase conjugate, Fast Blue B true FBbi:00000161 image FBbi:00000162 secondary antibody-alkaline phosphastase conjugate, Fast Red true FBbi:00000162 image FBbi:00000163 secondary antibody-alkaline phosphastase conjugate, INT true FBbi:00000163 image FBbi:00000164 secondary antibody-alkaline phosphastase conjugate, Magenta Phos true FBbi:00000164 image FBbi:00000165 secondary antibody-alkaline phosphastase conjugate, NABP true FBbi:00000165 image FBbi:00000166 secondary antibody-alkaline phosphastase conjugate, NAGP true FBbi:00000166 image FBbi:00000167 secondary antibody-alkaline phosphastase conjugate, NAMP true FBbi:00000167 image FBbi:00000168 secondary antibody-alkaline phosphastase conjugate, NATP true FBbi:00000168 image FBbi:00000169 secondary antibody-alkaline phosphastase conjugate, NBT true FBbi:00000169 image FBbi:00000170 secondary antibody-alkaline phosphastase conjugate, Vector Black true FBbi:00000170 image FBbi:00000171 secondary antibody-alkaline phosphastase conjugate, Vector Blue true FBbi:00000171 image FBbi:00000172 secondary antibody-alkaline phosphastase conjugate, Vector Red true FBbi:00000172 image FBbi:00000173 secondary antibody-alkaline phosphastase conjugate, BCIP true FBbi:00000173 image FBbi:00000174 secondary antibody-beta-galactosidase, X-Gal true FBbi:00000174 image FBbi:00000175 secondary antibody-beta-glucuronidase, X-gluc true FBbi:00000175 visualization of esterase conjugated to probe image FBbi:00000176 esterase FBbi:00000176 image FBbi:00000177 secondary antibody-esterase, Naphthol-AS-D-chloroacetate true FBbi:00000177 visualization of glucose oxidase conjugated to probe image FBbi:00000178 glucose oxidase FBbi:00000178 image FBbi:00000179 secondary antibody-glucose oxidase, TNBT true FBbi:00000179 image FBbi:00000180 secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine true FBbi:00000180 image FBbi:00000181 secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine silver enhanced true FBbi:00000181 image FBbi:00000182 secondary antibody-horseradish peroxidase, 4-chloro-1-naphthol true FBbi:00000182 image FBbi:00000183 secondary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole true FBbi:00000183 image FBbi:00000184 secondary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine true FBbi:00000184 image FBbi:00000185 secondary antibody-horseradish peroxidase, Vector NovaRed true FBbi:00000185 image FBbi:00000186 secondary antibody-horseradish peroxidase, Vector SG true FBbi:00000186 image FBbi:00000187 secondary antibody-horseradish peroxidase, Vector VIP true FBbi:00000187 image FBbi:00000188 secondary antibody-phosphatase, Naphthol-AS-BI-phosphate true FBbi:00000188 image FBbi:00000189 secondary antibody-fluor conjugate true FBbi:00000189 image FBbi:00000190 secondary antibody-Alexa Fluor conjugate true FBbi:00000190 visualization of aminomethylcoumarin conjugated to probe image AMCA FBbi:00000191 aminomethylcoumarin FBbi:00000191 visualization of Cascade blue conjugated to probe image FBbi:00000192 Cascade blue FBbi:00000192 image Cy2 FBbi:00000193 secondary antibody-cyanine conjugate true FBbi:00000193 image DTAF FBbi:00000194 secondary antibody-diaminotriazinylaminoflorescein conjugate true FBbi:00000194 image FITC FBbi:00000195 secondary antibody-fluorescein isothiocyanate conjugate true FBbi:00000195 image Cy3 FBbi:00000196 secondary antibody-indocarbocyanine conjugate true FBbi:00000196 image Cy5 FBbi:00000197 secondary antibody-indodicarbocyanine conjugate true FBbi:00000197 image LSRC FBbi:00000198 secondary antibody-lissamine rhodamine sulfonyl chloride true FBbi:00000198 image RRX FBbi:00000199 secondary antibody-rhodamine red-X conjugate true FBbi:00000199 image TRITC FBbi:00000200 secondary antibody-tetramethyl rhodamine isothiocyanate conjugate true FBbi:00000200 image TR FBbi:00000201 secondary antibody-Texas red conjugate true FBbi:00000201 visualization of gold conjugated to probe image FBbi:00000202 gold FBbi:00000202 image FBbi:00000203 labeled nucleic acid probe true FBbi:00000203 visualization of DNA probe image FBbi:00000204 DNA probe FBbi:00000204 image FBbi:00000205 biotin labeled DNA probe true FBbi:00000205 image FBbi:00000206 digoxigenin labeled DNA probe true FBbi:00000206 image FBbi:00000207 fluor labeled DNA probe true FBbi:00000207 image FBbi:00000208 BODIPY TR-14-dUTP labeled DNA probe true FBbi:00000208 image FBbi:00000209 bromodeoxyuridine labeled DNA probe true FBbi:00000209 image FBbi:00000210 fluoresceine-12-dUTP labeled DNA probe true FBbi:00000210 image FBbi:00000211 Oregon Green 488-5-dUTP labeled DNA probe true FBbi:00000211 image FBbi:00000212 radioisotope labeled DNA probe true FBbi:00000212 image FBbi:00000213 [32]P labeled DNA probe true FBbi:00000213 image FBbi:00000214 [33]P labeled DNA probe true FBbi:00000214 visualization of RNA probe image FBbi:00000215 RNA probe FBbi:00000215 image FBbi:00000216 biotin labeled RNA probe true FBbi:00000216 image FBbi:00000217 digoxigenin labeled RNA probe true FBbi:00000217 image FBbi:00000218 fluoroscein labeled RNA probe true FBbi:00000218 image FBbi:00000219 radioisotope labeled RNA probe true FBbi:00000219 image FBbi:00000220 [32]P labeled RNA probe true FBbi:00000220 image FBbi:00000221 [33]P labeled RNA probe true FBbi:00000221 image FBbi:00000222 imaging method FBbi:00000222 image FBbi:00000223 graphic illustration FBbi:00000223 image FBbi:00000224 computer graphic FBbi:00000224 image FBbi:00000225 black and white graphic FBbi:00000225 image FBbi:00000226 color graphic FBbi:00000226 image FBbi:00000227 grey scale graphic FBbi:00000227 image FBbi:00000228 camera lucida assisted graphic FBbi:00000228 image FBbi:00000229 free hand graphic FBbi:00000229 image FBbi:00000230 line art graphic FBbi:00000230 image FBbi:00000231 charcoal pencil graphic FBbi:00000231 image FBbi:00000232 colored pencil graphic FBbi:00000232 image FBbi:00000233 graphite pencil graphic FBbi:00000233 image black and white graphic FBbi:00000234 pen and ink graphic FBbi:00000234 image FBbi:00000235 painted graphic FBbi:00000235 image FBbi:00000236 acrylic painted graphic FBbi:00000236 image FBbi:00000237 oil painted graphic FBbi:00000237 image FBbi:00000238 pastel painted graphic FBbi:00000238 image FBbi:00000239 watercolor painted graphic FBbi:00000239 methods for imaging objects large enough to be observed by the unaided eye image FBbi:00000240 macroscopy FBbi:00000240 methods for forming images of objects too small to be observed with the unaided eye image FBbi:00000241 microscopy FBbi:00000241 image FBbi:00000242 wide field light micrograph true FBbi:00000242 image FBbi:00000243 bright-field microscopy FBbi:00000243 imaging with rejection of the unscattered illumination (removal of the zero order component of the diffracted wave) image FBbi:00000244 dark-field microscopy FBbi:00000244 image DIC Nomarski FBbi:00000245 differential interference contrast microscopy FBbi:00000245 image FBbi:00000246 fluorescence microscopy FBbi:00000246 image FBbi:00000247 phase contrast microscopy FBbi:00000247 image FBbi:00000248 polarization microscopy FBbi:00000248 image FBbi:00000249 time lapse microscopy FBbi:00000249 image FBbi:00000250 narrow field light micrograph true FBbi:00000250 image FBbi:00000251 confocal microscopy FBbi:00000251 image FBbi:00000252 single-spot confocal microscopy FBbi:00000252 image FBbi:00000253 spinning disk confocal microscopy FBbi:00000253 image FBbi:00000254 two-photon laser scanning microscopy FBbi:00000254 image FBbi:00000255 multi-photon microscopy FBbi:00000255 image mode of electron microscopy FBbi:00000256 electron microscopy FBbi:00000256 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) FBbi:00000257 image FBbi:00000258 transmission electron microscopy (TEM) FBbi:00000258 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 FBbi:00000259 http://en.wikipedia.org/wiki/X-ray_microscope image FBbi:00000260 X-ray microscopy FBbi:00000260 image FBbi:00000261 montage FBbi:00000261 Membrane permeabilization by the action of ionic or non-ionic detergents jm 2010-03-07T02:37:21Z image FBbi:00000262 detergent permeabilized FBbi:00000262 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 FBbi:00000263 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 FBbi:00000264 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 FBbi:00000265 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 FBbi:00000266 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 FBbi:00000267 sources and methods for illumination jm 2010-03-09T10:38:14Z image FBbi:00000268 illumination method FBbi:00000268 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 FBbi:00000269 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 FBbi:00000270 jm 2010-03-09T10:38:14Z image FBbi:00000271 contrast-enhancing method FBbi:00000271 jm 2010-03-09T10:46:27Z image FBbi:00000272 illumination by photons FBbi:00000272 jm 2010-03-09T10:46:27Z image FBbi:00000273 illumination by electrons FBbi:00000273 jm 2010-03-09T10:46:27Z image FBbi:00000274 illumination by acoustic waves FBbi:00000274 jm 2010-03-09T10:46:27Z image FBbi:00000275 illumination by neutrons FBbi:00000275 jm 2010-03-09T10:46:27Z image FBbi:00000276 illumination by ions FBbi:00000276 illumination that covers the entire field of view of the image-forming lens jm 2010-03-09T10:50:41Z image FBbi:00000277 widefield illumination FBbi:00000277 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 FBbi:00000278 jm 2010-03-09T10:50:41Z image FBbi:00000279 coherent illumination FBbi:00000279 jm 2010-03-09T10:50:41Z image FBbi:00000280 incoherent illumination FBbi:00000280 jm 2010-03-09T10:50:41Z image FBbi:00000281 nearfield illumination FBbi:00000281 jm 2010-03-09T10:50:41Z image FBbi:00000282 farfield illumination FBbi:00000282 jm 2010-03-09T10:50:41Z image FBbi:00000283 continuous illumination FBbi:00000283 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 FBbi:00000284 jm 2010-03-09T10:50:41Z image FBbi:00000285 oblique illumination FBbi:00000285 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 FBbi:00000286 illumination by multiple points of light simultaneously jm 2010-03-09T10:51:29Z image FBbi:00000287 multiple point scanning FBbi:00000287 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 FBbi:00000288 Multiple points of illumination generated by a fixed array of sources. jm 2010-03-09T10:52:38Z image FBbi:00000289 array scanning FBbi:00000289 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 FBbi:00000290 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 FBbi:00000291 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 FBbi:00000292 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 FBbi:00000293 jm 2010-03-09T11:33:49Z image FBbi:00000294 charge coupled device (CCD) FBbi:00000294 jm 2010-03-09T11:33:49Z image FBbi:00000295 photomultiplier tube (PMT) FBbi:00000295 jm 2010-03-09T11:33:49Z image FBbi:00000296 photodiode FBbi:00000296 jm 2010-03-09T11:33:49Z image FBbi:00000297 avalanche photodiode (APD) FBbi:00000297 jm 2010-03-09T11:33:49Z image FBbi:00000298 silicon intensified target tube (SIT) FBbi:00000298 jm 2010-03-09T11:33:49Z image FBbi:00000299 intensified SIT (ISIT) FBbi:00000299 jm 2010-03-09T11:33:49Z image FBbi:00000300 intensified CCD (ICCD) FBbi:00000300 jm 2010-03-09T11:33:49Z image FBbi:00000301 electron multiplying CCD (EMCCD) FBbi:00000301 jm 2010-03-09T11:33:49Z image FBbi:00000302 electron bombardment CCD (EBCCD) FBbi:00000302 jm 2010-03-09T11:33:49Z image FBbi:00000303 film FBbi:00000303 jm 2010-03-09T11:33:49Z image FBbi:00000304 complementary metal oxide semiconductor (CMOS) FBbi:00000304 jm 2010-03-09T11:33:49Z image FBbi:00000305 piezo-electric device FBbi:00000305 jm 2010-03-09T12:45:35Z image FBbi:00000306 wide-field detection FBbi:00000306 jm 2010-03-09T12:45:35Z image FBbi:00000307 narrow-field detection FBbi:00000307 jm 2010-03-09T03:11:47Z image FBbi:00000308 absorption of illumination FBbi:00000308 jm 2010-03-09T03:11:47Z image FBbi:00000309 inelastic scattering FBbi:00000309 jm 2010-03-09T03:11:47Z image FBbi:00000310 elastic scattering FBbi:00000310 jm 2010-03-09T03:11:47Z image FBbi:00000311 refractive index FBbi:00000311 jm 2010-03-09T03:11:47Z image FBbi:00000312 optical path length gradient FBbi:00000312 jm 2010-03-09T03:11:47Z image FBbi:00000313 retardance FBbi:00000313 jm 2010-03-09T03:11:47Z image FBbi:00000314 stiffness FBbi:00000314 jm 2010-03-09T03:11:47Z image FBbi:00000315 electron density FBbi:00000315 jm 2010-03-09T03:11:47Z image FBbi:00000316 fluorescence emission FBbi:00000316 jm 2010-03-09T03:11:47Z image FBbi:00000317 sub-nanosecond time-resolved fluorescence emission) FBbi:00000317 jm 2010-03-09T03:11:47Z image FBbi:00000318 fluorescence polarization (polarization angle resolved fluorescence emission) FBbi:00000318 jm 2010-03-09T03:11:47Z image FBbi:00000319 chemical composition FBbi:00000319 jm 2010-03-09T03:11:47Z image FBbi:00000320 elevation FBbi:00000320 methods for increasing the resolution beyond the classical Abbe diffraction limit jm 2010-03-09T03:12:34Z image FBbi:00000321 resolution-enhancing method FBbi:00000321 optical contrast enhancing method jm 2010-03-09T03:14:53Z image FBbi:00000322 optical method FBbi:00000322 computational contrast enhancing method jm 2010-03-09T03:14:53Z image FBbi:00000323 computational method FBbi:00000323 jm 2010-03-09T03:20:14Z image FBbi:00000324 in-focus phase contrast FBbi:00000324 jm 2010-03-09T03:20:14Z image FBbi:00000325 defocus phase contrast FBbi:00000325 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 FBbi:00000326 jm 2010-03-09T03:20:14Z image FBbi:00000327 Hoffman modulation FBbi:00000327 jm 2010-03-09T03:20:14Z image FBbi:00000328 single sideband edge enhancement (SSBE) FBbi:00000328 jm 2010-03-09T03:20:14Z image FBbi:00000329 interference reflection contrast (IRM) FBbi:00000329 jm 2010-03-09T03:20:14Z image FBbi:00000330 interference contrast FBbi:00000330 jm 2010-03-09T03:20:14Z image FBbi:00000331 polarization contrast FBbi:00000331 jm 2010-03-09T03:24:02Z image FBbi:00000332 structured illumination microscopy (SIM) FBbi:00000332 jm 2010-03-09T03:24:02Z image FBbi:00000333 point-localization method FBbi:00000333 jm 2010-03-09T03:24:02Z image FBbi:00000334 stimulated emission depletion (STED) FBbi:00000334 jm 2010-03-09T03:32:12Z image FBbi:00000335 PALM (photoactivation localization microscopy) FBbi:00000335 jm 2010-03-09T03:32:12Z image FBbi:00000336 STORM (stochastic optical reconstruction microscopy) FBbi:00000336 jm 2010-03-09T03:32:12Z image FBbi:00000337 FIONA (fluorescence imaging with one nanometer accuracy) FBbi:00000337 jm 2010-03-09T03:32:12Z image FBbi:00000338 DOPI (defocussed orientation and position imaging) FBbi:00000338 jm 2010-03-09T03:32:12Z image FBbi:00000339 PAINT (point accumulation for imaging in nanoscale topography) FBbi:00000339 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) FBbi:00000340 jm 2010-03-09T03:51:49Z image FBbi:00000341 UV/visible/IR illumination FBbi:00000341 jm 2010-03-09T03:51:49Z image FBbi:00000342 X-ray illumination FBbi:00000342 jm 2010-03-09T04:04:04Z image FBbi:00000343 microscopy with lenses FBbi:00000343 imaging by means of a physical probe that passes over the sample jm 2010-03-09T04:04:04Z image FBbi:00000344 scanning probe microscopy FBbi:00000344 jm 2010-03-09T04:18:03Z image mode of light microscopy FBbi:00000345 light microscopy FBbi:00000345 jm 2010-03-09T10:19:35Z image FBbi:00000347 scanning tunneling microscopy FBbi:00000347 jm 2010-03-09T10:19:35Z image FBbi:00000348 nearfield scanning optical microscopy (ANSOM) FBbi:00000348 Aperture-less NSOM. jm 2010-03-09T10:20:01Z image FBbi:00000349 ANSOM FBbi:00000349 jm 2010-03-09T10:23:41Z image FBbi:00000350 polarized light illumination FBbi:00000350 jm 2010-03-09T10:25:08Z image FBbi:00000351 orientation-independent polarization microscopy FBbi:00000351 jm 2010-03-09T10:27:11Z image FBbi:00000352 polarization-sensitive detection FBbi:00000352 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 FBbi:00000353 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 FBbi:00000354 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 FBbi:00000355 jm 2010-03-09T11:10:59Z image FBbi:00000356 Wiener filter FBbi:00000356 jm 2010-03-09T11:10:59Z image FBbi:00000357 3D-deconvolution FBbi:00000357 jm 2010-03-09T11:11:56Z image FBbi:00000358 no-neighbors deblurring FBbi:00000358 jm 2010-03-09T11:11:56Z image FBbi:00000359 nearest-neighbors deblurring FBbi:00000359 jm 2010-03-09T11:19:41Z image FBbi:00000360 constrained iterative deconvolution FBbi:00000360 jm 2010-03-09T11:19:41Z image FBbi:00000361 maximum likelihood deconvolution FBbi:00000361 jm 2010-03-09T11:19:41Z image FBbi:00000362 blind deconvolution FBbi:00000362 jm 2010-03-09T11:19:42Z image FBbi:00000363 exhaustive photon reassignment FBbi:00000363 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 FBbi:00000364 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 FBbi:00000365 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 FBbi:00000366 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 FBbi:00000367 jm 2010-03-11T10:09:33Z image FBbi:00000368 FLIM FBbi:00000368 single (or selective) plane illumination. jm 2010-03-11T10:09:33Z image FBbi:00000369 SPIM FBbi:00000369 coherent Raman anti-Stokes microscopy jm 2010-03-11T10:13:20Z image FBbi:00000370 CARS FBbi:00000370 optical coherence tomography; an interferometric method of imaging using back-scattered photons (elastic scattering) jm 2010-03-11T10:32:19Z image FBbi:00000371 OCT FBbi:00000371 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 FBbi:00000372 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 FBbi:00000373 jm 2010-03-12T08:54:56Z image FBbi:00000374 detection of photons FBbi:00000374 jm 2010-03-12T08:54:56Z image FBbi:00000375 detection of electrons FBbi:00000375 jm 2010-03-12T08:54:56Z image FBbi:00000376 detection of acoustic waves FBbi:00000376 jm 2010-03-12T08:54:56Z image FBbi:00000377 detection of current induced in the specimen FBbi:00000377 jm 2010-03-12T08:55:29Z image FBbi:00000378 detection of UV/visible/IR photons FBbi:00000378 jm 2010-03-12T08:55:29Z image FBbi:00000379 detection of X-ray photons FBbi:00000379 jm 2010-03-12T09:12:36Z image FBbi:00000380 scanning-transmission electron microscopy FBbi:00000380 jm 2010-03-12T09:16:40Z image EFTEM energy filtered TEM ESI electron spectroscopic imaging FBbi:00000381 EELS imaging FBbi:00000381 jm 2010-03-12T09:16:40Z image FBbi:00000382 EDAX imaging FBbi:00000382 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 FBbi:00000383 jm 2010-03-12T10:06:46Z image FBbi:00000384 photo-bleaching illumination FBbi:00000384 jm 2010-03-12T10:06:46Z image FBbi:00000385 photo-ablation illumination FBbi:00000385 jm 2010-03-12T10:06:46Z image FBbi:00000386 photo-switching illumination FBbi:00000386 jm 2010-03-12T10:06:46Z image FBbi:00000387 photo-activation illumination FBbi:00000387 jm 2010-03-12T10:06:46Z image FBbi:00000388 uncaging illumination FBbi:00000388 jm 2010-03-12T10:06:46Z image FBbi:00000389 trapping illumination FBbi:00000389 jm 2010-03-12T10:06:46Z image FBbi:00000390 emission-depletion illumination FBbi:00000390 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 FBbi:00000391 illumination and detection via a thin slit jm 2010-03-12T10:32:36Z image FBbi:00000392 slit-scan confocal microscopy FBbi:00000392 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 FBbi:00000393 jm 2010-03-12T10:39:24Z image FBbi:00000394 spot detector FBbi:00000394 jm 2010-03-12T10:39:24Z image FBbi:00000395 area detector FBbi:00000395 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 FBbi:00000396 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 FBbi:00000397 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 FBbi:00000398 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 FBbi:00000399 visualization of sequence-specific nucleic acid probe jm 2010-03-14T09:07:35Z image FBbi:00000400 sequence-specific nucleic acid probe FBbi:00000400 visualization of antibody jm 2010-03-14T09:07:35Z image FBbi:00000401 antibody FBbi:00000401 visualization of lectin jm 2010-03-14T09:07:35Z image FBbi:00000402 lectin FBbi:00000402 visualization of small-molecule probe jm 2010-03-14T09:07:35Z image FBbi:00000403 small-molecule probe FBbi:00000403 jm 2010-03-14T10:42:36Z image FBbi:00000404 fluorescent dextran fill FBbi:00000404 visualization of fluorescent protein tag jm 2010-03-14T10:54:20Z image FBbi:00000405 fluorescent protein tag FBbi:00000405 visualization of probes for nucleic acid jm 2010-03-14T09:25:57Z image FBbi:00000406 probes for nucleic acid FBbi:00000406 visualization of small genetically encoded tag jm 2010-03-14T11:10:25Z image FBbi:00000407 small genetically encoded tag FBbi:00000407 visualization of probe for protein jm 2010-03-14T09:25:57Z image FBbi:00000408 probe for protein FBbi:00000408 visualization of organelle-specific probe jm 2010-03-14T09:25:57Z image FBbi:00000409 organelle-specific probe FBbi:00000409 visualization of macromolecular probe jm 2010-03-14T09:26:11Z image FBbi:00000410 macromolecular probe FBbi:00000410 visualization of probe for mitochondria jm 2010-03-14T09:28:19Z image FBbi:00000411 probe for mitochondria FBbi:00000411 visualization of probe for endoplasmic reticulum jm 2010-03-14T09:28:19Z image FBbi:00000412 probe for endoplasmic reticulum FBbi:00000412 visualization of probe for Golgi jm 2010-03-14T09:28:19Z image FBbi:00000413 probe for Golgi FBbi:00000413 visualization of probe for lysosomes jm 2010-03-14T09:28:19Z image FBbi:00000414 probe for lysosomes FBbi:00000414 visualization of stain with broad specificity jm 2010-03-15T11:51:34Z image positive staining FBbi:00000415 stain with broad specificity FBbi:00000415 visualization of tetracysteine tag jm 2010-03-14T11:12:03Z image FBbi:00000416 tetracysteine tag FBbi:00000416 visualization of Hoechst 33258 jm 2010-03-14T09:33:18Z image FBbi:00000417 Hoechst 33258 FBbi:00000417 visualization of genetically encoded biotin tag jm 2010-03-14T11:12:03Z image FBbi:00000418 genetically encoded biotin tag FBbi:00000418 jm 2010-03-17T01:55:02Z image FBbi:00000419 freeze_fracture/freeze_etch FBbi:00000419 visualization of fluorescent protein derived from Aequorea victoria jm 2010-03-17T01:59:59Z image FBbi:00000420 fluorescent protein derived from Aequorea victoria FBbi:00000420 visualization of membrane-permeant probe jm 2010-03-14T09:33:53Z image FBbi:00000421 membrane-permeant probe FBbi:00000421 visualization of membrane impermeant probe jm 2010-03-14T09:33:53Z image FBbi:00000422 membrane impermeant probe FBbi:00000422 visualization of acridine homodimer jm 2010-03-14T09:42:34Z image FBbi:00000423 acridine homodimer FBbi:00000423 visualization of 7-amino-actinomycin D jm 2010-03-14T09:42:34Z image FBbi:00000424 7-amino-actinomycin D FBbi:00000424 visualization of conconavalin A jm 2010-03-14T09:48:57Z image FBbi:00000425 conconavalin A FBbi:00000425 visualization of wheat germ agglutinin jm 2010-03-14T09:48:57Z image FBbi:00000426 wheat germ agglutinin FBbi:00000426 visualization of Phaseolus vulgaris lectin PHA-L) jm 2010-03-14T09:48:57Z image FBbi:00000427 Phaseolus vulgaris lectin PHA-L) FBbi:00000427 visualization of Arachis hypogaea (PNA) jm 2010-03-14T09:48:57Z image FBbi:00000428 Arachis hypogaea (PNA) FBbi:00000428 visualization of Helix pomatia agglutinin jm 2010-03-14T09:48:57Z image FBbi:00000429 Helix pomatia agglutinin FBbi:00000429 visualization of soybean agglutinin jm 2010-03-14T09:48:57Z image FBbi:00000430 soybean agglutinin FBbi:00000430 visualization of cholera toxin B jm 2010-03-14T09:48:57Z image FBbi:00000431 cholera toxin B FBbi:00000431 visualization of peptide-nucleic acid probe jm 2010-03-14T09:52:30Z image FBbi:00000432 peptide-nucleic acid probe FBbi:00000432 visualization of fluorescent protein derived from Anthozoa jm 2010-03-17T01:59:59Z image FBbi:00000433 fluorescent protein derived from Anthozoa FBbi:00000433 visualization of optical highlighter jm 2010-03-17T01:59:59Z image FBbi:00000434 optical highlighter FBbi:00000434 visualization of Blue fluorescent protein from Aequorea victoria jm 2010-03-17T02:01:22Z image FBbi:00000435 Blue fluorescent protein from Aequorea victoria FBbi:00000435 visualization of Cyan fluorescent protein from Aequorea jm 2010-03-17T02:01:22Z image FBbi:00000436 Cyan fluorescent protein from Aequorea FBbi:00000436 visualization of Green fluorescent protein from Aequorea jm 2010-03-17T02:01:22Z image FBbi:00000437 Green fluorescent protein from Aequorea FBbi:00000437 visualization of DiIC16 jm 2010-03-14T10:15:00Z image FBbi:00000438 DiIC16 FBbi:00000438 visualization of Yellow fluorescent protein from Aequorea jm 2010-03-17T02:01:22Z image FBbi:00000439 Yellow fluorescent protein from Aequorea FBbi:00000439 visualization of Alexa Fluor 488 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000440 Alexa Fluor 488 FBbi:00000440 visualization of Alexa Fluor 546 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000441 Alexa Fluor 546 FBbi:00000441 visualization of Alexa Fluor 568 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000442 Alexa Fluor 568 FBbi:00000442 visualization of Alexa Fluor 555 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000443 Alexa Fluor 555 FBbi:00000443 visualization of Alexa Fluor 594 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000444 Alexa Fluor 594 FBbi:00000444 visualization of Alexa Fluor 610 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000445 Alexa Fluor 610 FBbi:00000445 visualization of Alexa Fluor 633 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000446 Alexa Fluor 633 FBbi:00000446 visualization of Alexa Fluor 647 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000447 Alexa Fluor 647 FBbi:00000447 visualization of Cy2 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000448 Cy2 FBbi:00000448 visualization of Cy3 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000449 Cy3 FBbi:00000449 visualization of Cy5 conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000450 Cy5 FBbi:00000450 visualization of Fluorescein (FITC) conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000451 Fluorescein (FITC) FBbi:00000451 visualization of Rhodamine conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000452 Rhodamine FBbi:00000452 fluorophore with ex/em 589/615 visualization of TexasRed conjugated to probe jm 2010-03-14T10:22:41Z image FBbi:00000453 TexasRed FBbi:00000453 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) FBbi:00000454 visualization of fluorescent label conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000455 fluorescent label FBbi:00000455 visualization of enzyme label conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000456 enzyme label FBbi:00000456 visualization of electron dense label conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000457 electron dense label FBbi:00000457 visualization of biotin conjugated to probe jm 2010-03-14T10:25:58Z image FBbi:00000458 biotin FBbi:00000458 visualization of affinity for specific proteins jm 2010-03-14T10:28:34Z image FBbi:00000459 affinity for specific proteins FBbi:00000459 visualization of non-specific protein affinity jm 2010-03-14T10:28:34Z image FBbi:00000460 non-specific protein affinity FBbi:00000460 visualization of AzuriteFP jm 2010-03-17T02:09:45Z image FBbi:00000461 AzuriteFP FBbi:00000461 visualization of SiriusFP jm 2010-03-17T02:09:45Z image FBbi:00000462 SiriusFP FBbi:00000462 visualization of non-immunological protein probe jm 2010-03-14T10:32:01Z image FBbi:00000463 non-immunological protein probe FBbi:00000463 visualization of alpha-bungarotoxin jm 2010-03-14T10:36:52Z image FBbi:00000464 alpha-bungarotoxin FBbi:00000464 visualization of botulinum toxin jm 2010-03-14T10:36:52Z image FBbi:00000465 botulinum toxin FBbi:00000465 visualization of tetrodotoxin jm 2010-03-14T10:37:23Z image FBbi:00000466 tetrodotoxin FBbi:00000466 visualization of batrachatoxin jm 2010-03-14T10:37:23Z image FBbi:00000467 batrachatoxin FBbi:00000467 visualization of CeruleanFP jm 2010-03-17T02:10:21Z image FBbi:00000468 CeruleanFP FBbi:00000468 visualization of CyPet jm 2010-03-17T02:10:21Z image FBbi:00000469 CyPet FBbi:00000469 visualization of SCFP jm 2010-03-17T02:10:21Z image FBbi:00000470 SCFP FBbi:00000470 visualization of EmeraldFP jm 2010-03-17T02:11:07Z image FBbi:00000471 EmeraldFP FBbi:00000471 visualization of SuperfolderFP jm 2010-03-17T02:11:07Z image FBbi:00000472 SuperfolderFP FBbi:00000472 visualization of T-SapphireFP jm 2010-03-17T02:11:07Z image FBbi:00000473 T-SapphireFP FBbi:00000473 visualization of CitrineFP jm 2010-03-17T02:14:30Z image FBbi:00000474 CitrineFP FBbi:00000474 visualization of SYFP jm 2010-03-17T02:14:30Z image FBbi:00000475 SYFP FBbi:00000475 visualization of TopazFP jm 2010-03-17T02:14:30Z image FBbi:00000476 TopazFP FBbi:00000476 visualization of VenusFP jm 2010-03-17T02:14:30Z image FBbi:00000477 VenusFP FBbi:00000477 visualization of yPet jm 2010-03-17T02:14:30Z image FBbi:00000478 yPet FBbi:00000478 visualization of Blue fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000479 Blue fluorescent proteins from Anthozoa FBbi:00000479 visualization of Cyan fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000480 Cyan fluorescent proteins from Anthozoa FBbi:00000480 visualization of Green fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000481 Green fluorescent proteins from Anthozoa FBbi:00000481 visualization of Orange fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000482 Orange fluorescent proteins from Anthozoa FBbi:00000482 visualization of Red fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000483 Red fluorescent proteins from Anthozoa FBbi:00000483 visualization of Far-red fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000484 Far-red fluorescent proteins from Anthozoa FBbi:00000484 visualization of Yellow fluorescent proteins from Anthozoa jm 2010-03-17T02:16:24Z image FBbi:00000485 Yellow fluorescent proteins from Anthozoa FBbi:00000485 visualization of mTagBFP jm 2010-03-17T02:16:38Z image FBbi:00000486 mTagBFP FBbi:00000486 visualization of AmCyanFP jm 2010-03-17T02:17:42Z image FBbi:00000487 AmCyanFP FBbi:00000487 visualization of mCyFP jm 2010-03-17T02:17:42Z image FBbi:00000488 mCyFP FBbi:00000488 visualization of mTFP1 jm 2010-03-17T02:17:42Z image FBbi:00000489 mTFP1 FBbi:00000489 visualization of TagCFP jm 2010-03-17T02:17:42Z image FBbi:00000490 TagCFP FBbi:00000490 visualization of AQ143 jm 2010-03-17T02:19:04Z image FBbi:00000491 AQ143 FBbi:00000491 visualization of HcRed-tandemFP jm 2010-03-17T02:19:04Z image FBbi:00000492 HcRed-tandemFP FBbi:00000492 visualization of KatushkaFP jm 2010-03-17T02:19:04Z image FBbi:00000493 KatushkaFP FBbi:00000493 visualization of mKateFP jm 2010-03-17T02:19:04Z image FBbi:00000494 mKateFP FBbi:00000494 visualization of mKate2FP jm 2010-03-17T02:19:04Z image FBbi:00000495 mKate2FP FBbi:00000495 visualization of mPlumFP jm 2010-03-17T02:19:04Z image FBbi:00000496 mPlumFP FBbi:00000496 visualization of tdKatuskaFP jm 2010-03-17T02:19:04Z image FBbi:00000497 tdKatuskaFP FBbi:00000497 visualization of tdRFP639 jm 2010-03-17T02:19:04Z image FBbi:00000498 tdRFP639 FBbi:00000498 visualization of AceFP jm 2010-03-17T02:20:00Z image FBbi:00000499 AceFP FBbi:00000499 visualization of Azami GreenFP jm 2010-03-17T02:20:00Z image FBbi:00000500 Azami GreenFP FBbi:00000500 visualization of CopGFP jm 2010-03-17T02:20:00Z image FBbi:00000501 CopGFP FBbi:00000501 visualization of mWasabiFP jm 2010-03-17T02:20:00Z image FBbi:00000502 mWasabiFP FBbi:00000502 visualization of TagGFP jm 2010-03-17T02:20:00Z image FBbi:00000503 TagGFP FBbi:00000503 visualization of TagGFP2 jm 2010-03-17T02:20:00Z image FBbi:00000504 TagGFP2 FBbi:00000504 visualization of ZsGreenFP jm 2010-03-17T02:20:00Z image FBbi:00000505 ZsGreenFP FBbi:00000505 visualization of DsRed-ExpressFP jm 2010-03-17T02:22:53Z image FBbi:00000506 DsRed-ExpressFP FBbi:00000506 visualization of DsRed-Express2FP jm 2010-03-17T02:22:53Z image FBbi:00000507 DsRed-Express2FP FBbi:00000507 visualization of DsRed-MaxFP jm 2010-03-17T02:22:53Z image FBbi:00000508 DsRed-MaxFP FBbi:00000508 visualization of DsRed-monomerFP jm 2010-03-17T02:22:53Z image FBbi:00000509 DsRed-monomerFP FBbi:00000509 visualization of DsRed2FP jm 2010-03-17T02:22:53Z image FBbi:00000510 DsRed2FP FBbi:00000510 visualization of dTomatoFP jm 2010-03-17T02:22:53Z image FBbi:00000511 dTomatoFP FBbi:00000511 visualization of Kusabira OrangeFP jm 2010-03-17T02:22:53Z image FBbi:00000512 Kusabira OrangeFP FBbi:00000512 visualization of Kusabira OrangeFP2 jm 2010-03-17T02:22:53Z image FBbi:00000513 Kusabira OrangeFP2 FBbi:00000513 visualization of mOrangeFP jm 2010-03-17T02:22:53Z image FBbi:00000514 mOrangeFP FBbi:00000514 visualization of mOrange2FP jm 2010-03-17T02:22:53Z image FBbi:00000515 mOrange2FP FBbi:00000515 visualization of TagRFP jm 2010-03-17T02:22:53Z image FBbi:00000516 TagRFP FBbi:00000516 visualization of TagRFP-T jm 2010-03-17T02:22:53Z image FBbi:00000517 TagRFP-T FBbi:00000517 visualization of tdTomatoFP jm 2010-03-17T02:22:53Z image FBbi:00000518 tdTomatoFP FBbi:00000518 visualization of turboRFP jm 2010-03-17T02:22:53Z image FBbi:00000519 turboRFP FBbi:00000519 visualization of AsRed2FP jm 2010-03-17T02:24:26Z image FBbi:00000520 AsRed2FP FBbi:00000520 visualization of eqFP611 jm 2010-03-17T02:24:26Z image FBbi:00000521 eqFP611 FBbi:00000521 visualization of HcRed1FP jm 2010-03-17T02:24:26Z image FBbi:00000522 HcRed1FP FBbi:00000522 visualization of JRedFP jm 2010-03-17T02:24:26Z image FBbi:00000523 JRedFP FBbi:00000523 visualization of mAppleFP jm 2010-03-17T02:24:26Z image FBbi:00000524 mAppleFP FBbi:00000524 visualization of mCherryFP jm 2010-03-17T02:24:26Z image FBbi:00000525 mCherryFP FBbi:00000525 visualization of mRasberryFP jm 2010-03-17T02:24:26Z image FBbi:00000526 mRasberryFP FBbi:00000526 visualization of mRFP1 jm 2010-03-17T02:24:26Z image FBbi:00000527 mRFP1 FBbi:00000527 visualization of mRubyFP jm 2010-03-17T02:24:26Z image FBbi:00000528 mRubyFP FBbi:00000528 visualization of mStrawberryFP jm 2010-03-17T02:24:26Z image FBbi:00000529 mStrawberryFP FBbi:00000529 visualization of tdRFP611 jm 2010-03-17T02:24:26Z image FBbi:00000530 tdRFP611 FBbi:00000530 visualization of PhiYFP jm 2010-03-17T02:25:15Z image FBbi:00000531 PhiYFP FBbi:00000531 visualization of TagYFP jm 2010-03-17T02:25:15Z image FBbi:00000532 TagYFP FBbi:00000532 visualization of TurboYFP jm 2010-03-17T02:25:15Z image FBbi:00000533 TurboYFP FBbi:00000533 visualization of ZsYellowFP jm 2010-03-17T02:25:15Z image FBbi:00000534 ZsYellowFP FBbi:00000534 visualization of fluorescent protein timer jm 2010-03-17T02:27:50Z image FBbi:00000535 fluorescent protein timer FBbi:00000535 visualization of photoactivatable fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000536 photoactivatable fluorescent protein FBbi:00000536 visualization of photoconvertible fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000537 photoconvertible fluorescent protein FBbi:00000537 visualization of photoconvertible/photoswitchable fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000538 photoconvertible/photoswitchable fluorescent protein FBbi:00000538 visualization of photoswitchable fluorescent protein jm 2010-03-17T02:27:50Z image FBbi:00000539 photoswitchable fluorescent protein FBbi:00000539 visualization of DsRed-ES FP jm 2010-03-17T02:29:47Z image FBbi:00000540 DsRed-ES FP FBbi:00000540 visualization of Fast-FT jm 2010-03-17T02:29:47Z image FBbi:00000541 Fast-FT FBbi:00000541 visualization of Medium-FT jm 2010-03-17T02:29:47Z image FBbi:00000542 Medium-FT FBbi:00000542 visualization of Slow-FT jm 2010-03-17T02:29:47Z image FBbi:00000543 Slow-FT FBbi:00000543 visualization of PA-GFP jm 2010-03-17T02:31:26Z image FBbi:00000544 PA-GFP FBbi:00000544 visualization of PA-CFP jm 2010-03-17T02:31:26Z image FBbi:00000545 PA-CFP FBbi:00000545 visualization of PA-mCherry1FP jm 2010-03-17T02:31:26Z image FBbi:00000546 PA-mCherry1FP FBbi:00000546 visualization of PA-mRFP jm 2010-03-17T02:31:26Z image FBbi:00000547 PA-mRFP FBbi:00000547 visualization of Phamret jm 2010-03-17T02:31:26Z image FBbi:00000548 Phamret FBbi:00000548 visualization of Dendra2FP jm 2010-03-17T02:32:35Z image FBbi:00000549 Dendra2FP FBbi:00000549 visualization of dEOSFP jm 2010-03-17T02:32:35Z image FBbi:00000550 dEOSFP FBbi:00000550 visualization of KaedeFP jm 2010-03-17T02:32:35Z image FBbi:00000551 KaedeFP FBbi:00000551 visualization of mEOS2FP jm 2010-03-17T02:32:35Z image FBbi:00000552 mEOS2FP FBbi:00000552 visualization of mKikGR jm 2010-03-17T02:32:35Z image FBbi:00000553 mKikGR FBbi:00000553 visualization of wtEOSFP jm 2010-03-17T02:32:35Z image FBbi:00000554 wtEOSFP FBbi:00000554 visualization of wtKIikGR jm 2010-03-17T02:32:35Z image FBbi:00000555 wtKIikGR FBbi:00000555 visualization of IrisFP jm 2010-03-17T02:32:44Z image FBbi:00000556 IrisFP FBbi:00000556 visualization of bsDronpa jm 2010-03-17T02:34:12Z image FBbi:00000557 bsDronpa FBbi:00000557 visualization of Dronpa jm 2010-03-17T02:34:12Z image FBbi:00000558 Dronpa FBbi:00000558 visualization of Dronpa-3 jm 2010-03-17T02:34:12Z image FBbi:00000559 Dronpa-3 FBbi:00000559 visualization of E2GFP jm 2010-03-17T02:34:12Z image FBbi:00000560 E2GFP FBbi:00000560 visualization of KFP1 jm 2010-03-17T02:34:12Z image FBbi:00000561 KFP1 FBbi:00000561 visualization of mTFP0.7 jm 2010-03-17T02:34:12Z image FBbi:00000562 mTFP0.7 FBbi:00000562 visualization of PadronFP jm 2010-03-17T02:34:12Z image FBbi:00000563 PadronFP FBbi:00000563 visualization of rsCherryFP jm 2010-03-17T02:34:12Z image FBbi:00000564 rsCherryFP FBbi:00000564 visualization of rsCherryRevFP jm 2010-03-17T02:34:12Z image FBbi:00000565 rsCherryRevFP FBbi:00000565 visualization of rsFastLimeFP jm 2010-03-17T02:34:12Z image FBbi:00000566 rsFastLimeFP FBbi:00000566 visualization of optically-dense stain jm 2010-04-27T10:29:56Z image FBbi:00000567 optically-dense stain FBbi:00000567 visualization of electron-dense stain jm 2010-04-27T10:29:56Z image FBbi:00000568 electron-dense stain FBbi:00000568 visualization of uranyl salt jm 2010-04-27T10:38:31Z image FBbi:00000569 uranyl salt FBbi:00000569 visualization of lead salt jm 2010-04-27T10:38:31Z image FBbi:00000570 lead salt FBbi:00000570 visualization of osmium tetroxide jm 2010-04-27T10:38:31Z image FBbi:00000571 osmium tetroxide FBbi:00000571 visualization of potassium permanganate jm 2010-04-27T10:38:31Z image FBbi:00000572 potassium permanganate FBbi:00000572 jm 2010-04-27T10:39:43Z image FBbi:00000573 uranium compound FBbi:00000573 jm 2010-04-27T10:39:43Z image FBbi:00000574 molybdenum compound FBbi:00000574 jm 2010-04-27T10:39:43Z image FBbi:00000575 tungsten compound FBbi:00000575 jm 2010-04-27T10:39:43Z image FBbi:00000576 aurothioglucose FBbi:00000576 jm 2010-04-28T06:06:52Z image FBbi:00000577 other negative stain FBbi:00000577 visualization of metabolically incorporated other radioisotope jm 2010-04-28T06:08:02Z image FBbi:00000578 other radioisotope FBbi:00000578 A fragment of a cell, subcellular organelle, or macromolecular complex. jm 2010-04-28T06:08:42Z image FBbi:00000579 isolated subcellular component FBbi:00000579 electrons generated by inelastic scattering of other radiation, the primary radiation. jm 2010-05-04T12:25:14Z image FBbi:00000580 secondary electron generation FBbi:00000580 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 FBbi:00000581 data as acquired, with no alterations that change the pixel values. jm 2010-05-04T12:42:17Z image FBbi:00000582 unprocessed raw data FBbi:00000582 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 FBbi:00000583 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 FBbi:00000584 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) FBbi:00000585 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 FBbi:00000586 jm 2010-09-03T08:42:47Z image FBbi:00000587 elastic scattering of photons FBbi:00000587 jm 2010-09-03T08:43:42Z image FBbi:00000588 inelastic scattering of electrons FBbi:00000588 jm 2010-09-03T08:43:42Z image FBbi:00000589 inelastic scattering of photons (Raman scattering) FBbi:00000589 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 FBbi:00000590 jm 2010-09-03T09:55:12Z image FBbi:00000591 differences in chemical composition FBbi:00000591 jm 2010-09-03T09:55:12Z image FBbi:00000592 distribution of epitope FBbi:00000592 jm 2010-09-03T09:55:12Z image FBbi:00000593 form birefringence FBbi:00000593 jm 2010-09-03T09:55:12Z image FBbi:00000594 intrinsic birefringence FBbi:00000594 jm 2010-09-03T09:55:12Z image FBbi:00000595 stress-induced birefringence FBbi:00000595 jm 2010-09-03T09:55:12Z image FBbi:00000596 distribution of a specific nucleic acid sequence FBbi:00000596 jm 2010-09-03T09:55:12Z image FBbi:00000597 distribution of a specific protein FBbi:00000597 jm 2010-09-03T09:55:12Z image FBbi:00000598 differences in adsorption or binding of stain FBbi:00000598 jm 2010-09-03T09:55:12Z image FBbi:00000599 boundaries between regions with different refractive index FBbi:00000599 jm 2010-09-03T09:55:12Z image FBbi:00000600 differences in amount of elastic light scattering FBbi:00000600 jm 2010-09-04T11:57:06Z image FBbi:00000601 differences in deposition of metal shadow FBbi:00000601 jm 2010-09-04T12:55:54Z image FBbi:00000602 differences in intrinsic optical density FBbi:00000602 jm 2010-09-04T01:28:20Z image FBbi:00000603 fluorescence polarization microscopy FBbi:00000603 jm 2010-09-04T01:31:54Z image FBbi:00000604 compartmentalization of stain or label FBbi:00000604 jm 2010-09-04T01:35:37Z image FBbi:00000605 differences in fluorescence lifetime FBbi:00000605 jm 2010-09-04T01:36:45Z image FBbi:00000606 differences in orientation of fluorophore FBbi:00000606 jm 2010-09-04T01:51:14Z image FBbi:00000607 intrinsic mass distribution FBbi:00000607 jm 2010-09-04T02:05:02Z image FBbi:00000608 X-ray fluorescence FBbi:00000608 jm 2010-09-04T11:49:25Z image FBbi:00000609 heat fixed tissue FBbi:00000609 visualization of copper salt jm 2010-09-04T11:56:02Z image FBbi:00000610 copper salt FBbi:00000610 jm 2010-09-28T04:35:54Z image FBbi:00000611 dispersed cells in vitro FBbi:00000611 visualization of fluorescent protein derived from Arabidopsis jm 2011-05-23T09:33:44Z image FBbi:00000612 fluorescent protein derived from Arabidopsis FBbi:00000612 jm 2011-05-23T09:49:58Z image FBbi:00000613 vidicon tube camera FBbi:00000613 visualization of phototropin 2 jm 2011-05-23T09:55:54Z image FBbi:00000614 phototropin 2 FBbi:00000614 visualization of miniSOG jm 2011-05-23T09:57:01Z image FBbi:00000615 miniSOG FBbi:00000615 jm 2011-05-23T10:09:41Z image FTIR frustrated total internal reflection FBbi:00000616 evanescent wave scattering FBbi:00000616 jm 2011-05-23T10:10:58Z image total internal reflection fluorescence TIRF FBbi:00000617 evanescent wave microscopy FBbi:00000617 jm 2011-05-23T10:34:07Z image FBbi:00000618 ground state depletion scanning (GSD) FBbi:00000618 jm 2011-05-23T10:43:15Z image FBbi:00000619 nearfield illumination FBbi:00000619 jm 2011-05-23T10:44:03Z image FBbi:00000620 nearfield illumination FBbi:00000620 jm 2011-05-23T10:51:16Z image FBbi:00000621 freeze-substituted tissue FBbi:00000621 jm 2011-05-23T10:53:45Z image FBbi:00000622 high-voltage electron microscopy (HVEM) FBbi:00000622 jm 2011-05-23T10:53:45Z image FBbi:00000623 intermediate voltage electron microacopy (IVEM) FBbi:00000623 An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination. image FBbi:00001000 radiography FBbi:00001000 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 FBbi:00001001 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 FBbi:00001002 Tomography using X-ray illumination. image FBbi:00001003 X-ray tomography FBbi:00001003 An imaging technique that creates virtual sections through the use of any kind of penetrating wave. image FBbi:00001004 tomography FBbi:00001004 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 FBbi:00001005 image FBbi:00001006 x-ray/gamma ray illumination FBbi:00001006 image FBbi:00001007 gamma ray illumination FBbi:00001007 image FBbi:00001012 fixation method FBbi:00001012 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) FBbi:00050000 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 FBbi_root:00000000 GO:0003674 molecular process molecular_function GO:0003824 catalytic activity GO:0008150 biological_process true GO:0016301 kinase activity GO:0016740 transferase activity GO:0016772 transferase activity, transferring phosphorus-containing groups owl:Nothing owl:Thing 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 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) 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).