Biological entities in BEL are represented by BEL Terms. Two categories of biological entities are represented in BEL: classes of abundances and classes of processes.
Measured values in life science experiments are often measurements of the abundance of a type of thing in a given sample or set of samples. For example, a probe value measured by a microarray provides a measure of the abundance of RNA matching the probe in the sample, and an appropriate set of probe values may be interpreted as a measure of the abundance of the RNA produced by a specific gene.
Some BEL 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”.
Some BEL Terms may represent classes of complex phenomena taking place at the level of the cell or the organism, such as the process of cell cycle or the process of a disease such as cardiomyopathy. In other cases, BEL Terms may represent classes of specific molecular activities, such as a type of reaction involving small molecules or the kinase activity of a class of proteins.
Measurable biological parameters such as systolic blood pressure or body temperature do not correspond to abundances, and can be accommodated by representation as process BEL Terms. These BEL Terms thereby 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 V1.0 specifies a set of over 30 intrinsic functions allowed in term expressions.
The combination of a term function and its arguments fully specifies a represented biological entity. The BEL Term expression f(a) denotes a BEL Term defined by function f() applied to an argument a. Wherever the same function applied to the same arguments is defined, BEL assumes these BEL Terms denote the same biological entity.
The semantics of a BEL Term are determined by the definition of the function used in the term expression. For example, the function proteinAbundance() is defined such that any expression using proteinAbundance() represents a class of abundance of protein. Many functions used in BEL take only single values as arguments and provide a structured method of adopting ontologies and vocabularies for use in BEL. For example, values in the HUGO Gene Nomenclature Committee (HGNC) vocabulary of official human gene names 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 corresponding gene. Thus, we might encode the BEL Term proteinAbundance(AKT1).
Term Disambiguation via Namespaces
As gene symbols, and more generally, names in life sciences as a rule are often ambiguous, it is more precise to reference the vocabulary as well as the symbol when designating a term identifying an abundance or biological process. To this end, we would prefer to write proteinAbundance(HGNC:AKT1) so that we can provide an exact specification of the protein abundance being referenced.
The designation of a term parameter such as AKT1 referenced with respect to an external ontology, HGNC in this case, is central to the BEL language. Generally, all term parameters are defined within a Namespace identifying the vocabulary used to identify the term parameter. BEL provides the ability to use existing namespaces or to create your own namespaces.