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The following BEL functions represent transformations. Transformations are processes or events in which one class of abundance is transformed or changed into a second class of abundance by translocation, degradation, or participation in a reaction. All types of abundance terms except componsiteAbundance() may be used within these transformation functions.

Translocations

BEL translocation functions include translocation() as well as cellSurfaceExpression() and cellSecretion(), two functions intended to provide a simple, standard means of expressing commonly represented translocations.

translocation(), tloc()

For the abundance term A, translocation(<abundance>, fromLoc(ns1:v1), toLoc(ns2:v2)) or tloc(<abundance>, fromLoc(ns1:v1), toLoc(ns2:v2)) denotes the frequency or number of events in which members of <abundance> move from the location designated by the value v1 in the namespace ns1 to the location designated by the value v2 in the namespace ns2. Translocation is applied to represent events on the cellular scale, like endocytosis, protein secretion (see cellSecretion()), and movement of transcription factors from the cytoplasm to the nucleus.

Example

endocytosis (translocation from the cell surface to the endosome) of the epidermal growth factor receptor (EGFR) protein can be represented as:

tloc(p(HGNC:EGFR), fromLoc(GOCC:"cell surface"), toLoc(GOCC:endosome))

cellSecretion(), sec()

For the abundance term A, cellSecretion(<abundance>) or sec(<abundance>) denotes the frequency or number of events in which members of <abundance> move from cells to regions outside of the cells. cellSecretion(<abundance>) can be equivalently expressed as:

tloc(<abundance>, fromLoc(GOCC:intracellular), toLoc(GOCC:"extracellular space"))

The intent of the cellSecretion() function is to provide a simple, standard means of expressing a commonly represented translocation.

cellSurfaceExpression(), surf()

cellSurfaceExpression(<abundance>) or surf(<abundance>) denotes the frequency or abundance of events in which members of <abundance> move to the surface of cells. cellSurfaceExpression(<abundance>) can be equivalently expressed as:

tloc(<abundance>, fromLoc(GOCC:intracellular), toLoc(GOCC:"cell surface"))

The intent of the cellSurfaceExpression() function is to provide a simple, standard means of expressing a commonly represented translocation.

degradation(), deg()

degradation(<abundance>) or deg(<abundance>) denotes the frequency or number of events in which a member of <abundance> is degraded in some way such that it is no longer a member of <abundance>. For example, degradation() is used to represent proteasome-mediated proteolysis. The BEL Framework automatically connects deg(<abundance>) to <abundance> such that:

deg(<abundance>) directlyDecreases <abundance>

reaction(), rxn()

reaction(reactants(<abundance term list1>), products(<abundance term list2>) ) denotes the frequency or abundance of events in which members of the abundances in <abundance term list1> (the reactants) are transformed into members of the abundances in <abundance term list2> (the products).

Example

The reaction in which superoxides are dismutated into oxygen and hydrogen peroxide can be represented as:

rxn(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide"), a(CHEBI: "oxygen"))

 

 

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