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)
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
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
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
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.
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
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
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.
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
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
The child is an essential component of the parent device, or plays an essential role in performance of the parent function.
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
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
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.
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.
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.
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
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
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.
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.
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.
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.
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.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
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
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
Terry Meehan
This is the transitive form of the develops from relation
develops from
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
Regulation precludes parthood; the regulatory process may not be within the regulated process.
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.
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.
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.
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)".
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.
capable of part of
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.
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.
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
has developmental contribution from
inverse of has developmental contribution from
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
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.
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.
developmentally succeeded by
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
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
A mereological relationship or a topological relationship
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)
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
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.
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.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
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).
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
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
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
has potential to directly develop into
causally downstream of
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.
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
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.
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
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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
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.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
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.
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.
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.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
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.
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.
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.
directly positively regulates activity of
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.
A relationship between a material entity and a process where the material entity has some causal role that influences the 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.
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
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).
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.
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
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.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
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.
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)
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)
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
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
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
causally upstream of or within, negative effect
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.
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
anatomical entity
ethylene glycol-bis-succinimidyl succinate fixed tissue
Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state.
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.
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 nitro blue tetrazolium chloride
visualization of cationic colloidal gold
visualization of CMX rosamine (Mitotracker Red)
visualization of DiOC6 (3,3'-dihexyloxacarbocyanine iodide)
DiOC6 (3,3'-dihexyloxacarbocyanine iodide)
visualization of 4',6-diamidino-2-phenylindole (DAPI)
endogenous substrate, acidotropic-fluor conjugate
endogenous substrate, lectin-fluor conjugate
endogenous substrate, lectin-gold conjugate
endogenous substrate, phalloidin-fluor conjugate
visualization of genetically encoded enzyme
visualization of genetically encoded tag
Aequorea victoria red fluorescent protein tag
visualization of the connected regions of a cell by filling with a label
Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C
Tissue treated to make cell membranes permeable, typically for the purpose of allowing access by exogenous stains or substrates.
visualization of metabolically incorporated radioisotope
visualization of metabolically incorporated [14]C
visualization of metabolically incorporated [32]P
visualization of metabolically incorporated [33]P
visualization of metabolically incorporated [35]S
visualization of metabolically incorporated [3]H
vizualization of label conjugated to probe
tissue made permeable by the action of glycerol
visualization of labeled primary antibody
primary antibody-enzyme conjugate, substrate
visualization of alkaline phosphatase conjugated to probe
primary antibody-alkaline phosphastase conjugate, DAB
primary antibody-alkaline phosphastase conjugate, ELF 97 phosphate
primary antibody-alkaline phosphastase conjugate, Vector Black
primary antibody-alkaline phosphastase conjugate, Vector Blue
primary antibody-alkaline phosphastase conjugate, Vector Red
visualization of horseradish peroxidase conjugated to probe
primary antibody-horseradish peroxidase, 4-chloro-1-naphthol
primary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole
primary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine
primary antibody-horseradish peroxidase, Vector NovaRed
primary antibody-horseradish peroxidase, Vector SG
primary antibody-horseradish peroxidase, Vector VIP
primary antibody-aminomethylcoumarin acetate
primary antibody-fluorescein isothiocyanate
primary antibody-tetramethyl rhodamine isothiocyanate
visualization of primary antibody plus labeled secondary antibody
primary antibody plus labeled secondary antibody
secondary antibody-enzyme conjugate, substrate
visualization of acid phosphatase conjugated to probe
secondary antibody-alkaline phosphastase conjugate, DAB
secondary antibody-alkaline phosphastase conjugate, ELF 97 phosphate
secondary antibody-alkaline phosphastase conjugate, Fast Blue B
secondary antibody-alkaline phosphastase conjugate, Fast Red
secondary antibody-alkaline phosphastase conjugate, INT
secondary antibody-alkaline phosphastase conjugate, Magenta Phos
secondary antibody-alkaline phosphastase conjugate, NABP
secondary antibody-alkaline phosphastase conjugate, NAGP
secondary antibody-alkaline phosphastase conjugate, NAMP
secondary antibody-alkaline phosphastase conjugate, NATP
secondary antibody-alkaline phosphastase conjugate, NBT
secondary antibody-alkaline phosphastase conjugate, Vector Black
secondary antibody-alkaline phosphastase conjugate, Vector Blue
secondary antibody-alkaline phosphastase conjugate, Vector Red
secondary antibody-alkaline phosphastase conjugate, BCIP
secondary antibody-beta-galactosidase, X-Gal
secondary antibody-beta-glucuronidase, X-gluc
visualization of esterase conjugated to probe
secondary antibody-esterase, Naphthol-AS-D-chloroacetate
visualization of glucose oxidase conjugated to probe
secondary antibody-glucose oxidase, TNBT
secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine
secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine silver enhanced
secondary antibody-horseradish peroxidase, 4-chloro-1-naphthol
secondary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole
secondary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine
secondary antibody-horseradish peroxidase, Vector NovaRed
secondary antibody-horseradish peroxidase, Vector SG
secondary antibody-horseradish peroxidase, Vector VIP
secondary antibody-phosphatase, Naphthol-AS-BI-phosphate
secondary antibody-Alexa Fluor conjugate
visualization of aminomethylcoumarin conjugated to probe
visualization of Cascade blue conjugated to probe
secondary antibody-diaminotriazinylaminoflorescein conjugate
secondary antibody-fluorescein isothiocyanate conjugate
secondary antibody-indocarbocyanine conjugate
secondary antibody-indodicarbocyanine conjugate
secondary antibody-lissamine rhodamine sulfonyl chloride
secondary antibody-rhodamine red-X conjugate
secondary antibody-tetramethyl rhodamine isothiocyanate conjugate
visualization of gold conjugated to probe
Oregon Green 488-5-dUTP labeled DNA probe
methods for imaging objects large enough to be observed by the unaided eye
methods for forming images of objects too small to be observed with the unaided eye
imaging with rejection of the unscattered illumination (removal of the zero order component of the diffracted wave)
differential interference contrast microscopy
image is formed by scanning the surface of the specimen with a beam of electrons in a raster pattern
the scanning probe is maintained at a fixed distance above the surface e of the specimen by van der Waals forces
Membrane permeabilization by the action of ionic or non-ionic detergents
permeabilization due to extraction of lipid from membranes by an organic solvent such as acetone or methanol.
Saponin, a detergent-like molecule, preferentially forms holes in membranes that contain cholesterol.
methods and devices used for capturing an image of a real object; distinct from images created by artwork
methods and devices used for creating images by some form of artwork, as distinct from capturing images by means of some recording device
A form of graphical illustration that changes with time to give a sense of motion or represent dynamic changes in the portrayal.
media and devices employed for recording the alterations in the illumination that result from its interaction with the sample
The physical property of the specimen that leads to the modifications of the illumination that are recorded in the image.
illumination that covers the entire field of view of the image-forming lens
illumination restricted to a small portion of the field of view of the imaging lens; often one or more diffraction limited spots
illumination that varies with time; often achieved with pulsed lasers for the purpose of generating very-high peak illumination power
illumination by a single spot of light that is scanned across the field of view
illumination by multiple points of light simultaneously
scanning by multiple points of light arising from pinholes in a spinning disk that is illuminated by a widefield source
Multiple points of illumination generated by a fixed array of sources.
illumination parallel or at small angles to the optical axis is attenuated or blocked by a stop
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
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
complementary metal oxide semiconductor (CMOS)
sub-nanosecond time-resolved fluorescence emission)
fluorescence polarization (polarization angle resolved fluorescence emission)
methods for increasing the resolution beyond the classical Abbe diffraction limit
a birefringent optical element typically used to split polarized illumination into two sets of parallel but displaced rays
structured illumination microscopy (SIM)
PALM (photoactivation localization microscopy)
STORM (stochastic optical reconstruction microscopy)
FIONA (fluorescence imaging with one nanometer accuracy)
DOPI (defocussed orientation and position imaging)
PAINT (point accumulation for imaging in nanoscale topography)
structured illumination used at sufficiently high power to cause significant ground-state depletion of the imaged fluorophore, thus allowing for non-linear resolution enhancement
saturated structured-illumination microscopy (SSIM)
imaging by means of a physical probe that passes over the sample
nearfield scanning optical microscopy (ANSOM)
orientation-independent polarization microscopy
Uses an objective with extra components to manipulate the wave front in the plane of the objective aperture.
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
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
illumination in the form of a thin sheet of light directed perpendicular to the optic axis
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.
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.
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.
single (or selective) plane illumination.
optical coherence tomography; an interferometric method of imaging using back-scattered photons (elastic scattering)
image created using the electrons generated by ionization of a sample due to inelastic scattering of the primary beam of radiation
imaged formed using electrons undergoing elastic scattering at very high angles, with emission of characteristic X-rays
detection of current induced in the specimen
scanning-transmission electron microscopy
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
illumination in the shape of a thin line that is swept over the field of view
illumination and detection via a thin slit
Fixed array of sources focused to an array of spots that is swept over the specimen in raster fashion
methods of visualization that differentiate between different regions or surfaces of the specimen based on contiguity
methods of visualization that differentiate regions of the specimen on the basis of their chemical properties
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)
visualization by exclusion of a stain in which the specimen is immersed; compare with "positive staining.
visualization of sequence-specific nucleic acid probe
visualization of fluorescent protein tag
visualization of probes for nucleic acid
visualization of small genetically encoded tag
visualization of organelle-specific probe
visualization of probe for endoplasmic reticulum
visualization of stain with broad specificity
visualization of genetically encoded biotin tag
visualization of fluorescent protein derived from Aequorea victoria
fluorescent protein derived from Aequorea victoria
visualization of membrane-permeant probe
visualization of membrane impermeant probe
visualization of Phaseolus vulgaris lectin PHA-L)
visualization of Helix pomatia agglutinin
visualization of peptide-nucleic acid probe
visualization of fluorescent protein derived from Anthozoa
fluorescent protein derived from Anthozoa
visualization of Blue fluorescent protein from Aequorea victoria
Blue fluorescent protein from Aequorea victoria
visualization of Cyan fluorescent protein from Aequorea
visualization of Green fluorescent protein from Aequorea
visualization of Yellow fluorescent protein from Aequorea
Yellow fluorescent protein from Aequorea
visualization of Alexa Fluor 488 conjugated to probe
visualization of Alexa Fluor 546 conjugated to probe
visualization of Alexa Fluor 568 conjugated to probe
visualization of Alexa Fluor 555 conjugated to probe
visualization of Alexa Fluor 594 conjugated to probe
visualization of Alexa Fluor 610 conjugated to probe
visualization of Alexa Fluor 633 conjugated to probe
visualization of Alexa Fluor 647 conjugated to probe
visualization of Cy2 conjugated to probe
visualization of Cy3 conjugated to probe
visualization of Cy5 conjugated to probe
visualization of Fluorescein (FITC) conjugated to probe
visualization of Rhodamine conjugated to probe
visualization of TexasRed conjugated to probe
fluorophore derivative of rhodamine with ex/em 547/572
visualization of Tetramethyl rhodamine (TRITC) conjugated to probe
visualization of fluorescent label conjugated to probe
visualization of enzyme label conjugated to probe
visualization of electron dense label conjugated to probe
visualization of biotin conjugated to probe
visualization of affinity for specific proteins
visualization of non-specific protein affinity
visualization of non-immunological protein probe
visualization of Blue fluorescent proteins from Anthozoa
visualization of Cyan fluorescent proteins from Anthozoa
visualization of Green fluorescent proteins from Anthozoa
Green fluorescent proteins from Anthozoa
visualization of Orange fluorescent proteins from Anthozoa
Orange fluorescent proteins from Anthozoa
visualization of Red fluorescent proteins from Anthozoa
visualization of Far-red fluorescent proteins from Anthozoa
Far-red fluorescent proteins from Anthozoa
visualization of Yellow fluorescent proteins from Anthozoa
Yellow fluorescent proteins from Anthozoa
visualization of fluorescent protein timer
visualization of photoactivatable fluorescent protein
visualization of photoconvertible fluorescent protein
visualization of photoconvertible/photoswitchable fluorescent protein
photoconvertible/photoswitchable fluorescent protein
visualization of photoswitchable fluorescent protein
visualization of metabolically incorporated other radioisotope
A fragment of a cell, subcellular organelle, or macromolecular complex.
electrons generated by inelastic scattering of other radiation, the primary radiation.
specimen from which water has been removed by a process that avoids liquid-gas and solid-gas phase transitions.
data as acquired, with no alterations that change the pixel values.
specimen from which water has been removed by evaporation under vacuum at a temperature below freezing.
fluorophore derivative of rhodamine with ex/em 580/605
visualization of X-Rhodamine conjugated to probe
A method of reconstructing 3D structure by combining serial sectioning with scanning EM.
inelastic scattering of photons (Raman scattering)
The source of the variation in the imaged parameter across the field of view.
distribution of a specific nucleic acid sequence
differences in adsorption or binding of stain
boundaries between regions with different refractive index
differences in amount of elastic light scattering
differences in deposition of metal shadow
differences in intrinsic optical density
differences in orientation of fluorophore
visualization of fluorescent protein derived from Arabidopsis
fluorescent protein derived from Arabidopsis
FTIR frustrated total internal reflection
total internal reflection fluorescence TIRF
intermediate voltage electron microacopy (IVEM)
An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination.
An imaging technique that creates virtual sections through the use of any kind of penetrating wave.
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.
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.
focussed ion beam scanning electron microscopy (FIB-SEM)
transferase activity, transferring phosphorus-containing groups
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
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'
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'
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).