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Reactions

The reaction() or rxn() function expresses the transformation of products into reactants, each defined by a list of abundances. For example:

reaction(reactants(abundance(CHEBI:phophoenolpyruvate), abundance(CHEBI:ADP)),\ 
 products(abundance(CHEBI:pyruvate), abundance(CHEBI:ATP)))

short form:

rxn(reactants(a(CHEBI:phophoenolpyruvate), a(CHEBI:ADP)),\
 products(a(CHEBI:pyruvate), a(CHEBI:ATP)))

This BEL Term represents the reaction in which the reactants phosphoenolpyruvate and ADP are converted into pyruvate and ATP.

Translocations

Translocations, or the movement of abundances from one location to another, are represented in BEL Terms by the translocation() or tloc() function. For convenience, the frequently used translocations of abundances from inside the cell to cell surface or extracellular space are represented by the cellSurface() and cellSecretion() functions, respectively. The following term represents the event in which human NFE2L2 protein is translocated from the cytoplasm to the nucleus:

translocation(proteinAbundance(HGNC:NFE2L2), MESHCL:Cytoplasm, MESHCL:"Cell Nucleus")

short form:

tloc(p(HGNC:NFE2L2), MESHCL:Cytoplasm, MESHCL:"Cell Nucleus")

The translocation() function requires arguments for both the starting and ending locations.

In cases where the starting location is not known, but is within the cell, the general MeSH term "Intracellular Space" can be used. For example:

tloc(p(HGNC:NFE2L2), MESH:"Intracellular Space", MESH:"Cell Nucleus")

Secretion of mouse IL6 protein can be represented by:

cellSecretion(proteinAbundance(MGI:Il6))

short form:

sec(p(MGI:Il6))

Cell surface expression of rat Fas can be represented by:

cellSurface(proteinAbudance(RGD:Fas))

short form:

surf(p(RGD:Fas))

Degradation

Events in which an abundance is degraded can be represented by the degradation() or deg() function. For example:

degradation(rnaAbundance(HGNC:MYC))

short form:

deg(r(HGNC:MYC))

This term represents the degradation of the human MYC RNA. Degradation decreases the amount of the abundance - when degradation statements are compiled, a directlyDecreases relationship edge is added between the degradation term and the degraded entity.

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