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Two general categories of biological entities are represented as BEL Terms: abundances and processes.

Abundances

Life science experiments often measure the abundance of a type of thing in a given sample or set of samples. BEL Abundance Terms represent classes of abundance, the abundances of specific types of things. Examples include the protein abundance of TP53, the RNA abundance of CCND1, the abundance of the protein AKT1 phosphorylated at serine 21, or the abundance of the complex of the proteins CCND1 and CDK4.

Processes

BEL Process Terms represent classes of complex phenomena taking place at the level of the cell or the organism, such as the biological process of cell cycle or a disease process such as Cardiomyopathy. In other cases, BEL Terms may represent classes of specific molecular activities, such as the kinase activity of the AKT1 protein, or a specific chemical reaction like conversion of superoxides to hydrogen peroxide and oxygen.

Measurable biological parameters such as Blood Pressure or Body Temperature are represented as process BEL Terms. These BEL Terms denote biological activities that, when measured, are reduced to an output parameter.

BEL Terms as Functional Expressions

BEL Terms are denoted by expressions composed of a BEL Function and a list of arguments. BEL v2.0 specifies a set of approximately 20 functions allowed in term expressions.

The combination of a BEL function and its arguments fully specifies a BEL Term. The BEL Term expression f(a) denotes a BEL Term defined by function f() applied to an argument a. Wherever the same function is applied to the same arguments, the resulting BEL Term references the same biological entity.

The semantics of a BEL Term are determined by the function used in the term expression. For example, the function proteinAbundance() is defined such that any term expression using proteinAbundance() represents a class of abundance of protein. Many BEL functions take only single values as arguments, providing a structured method of using ontologies and vocabularies in BEL. For example, values in the HUGO Gene Nomenclature Committee (HGNC) vocabulary of official human gene symbols can be used to designate gene, RNA, and protein abundances. The function proteinAbundance() could then be applied to an HGNC gene symbol, AKT1 for example, to indicate the class of protein abundances produced by the AKT1 gene, producing the BEL Term proteinAbundance(HGNC:AKT1).

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