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Terminology

BEL

BEL stands for Biological Expression Language. BEL is a means of capturing biological knowledge in a manner that is human friendly and convertable into a computatable format for supporting knowledge driven analytics. It also serves as a format to share biological knowledge using an open standard.

OpenBEL

OpenBEL is the name for the open source effort to support BEL. It includes the open source community supporting BEL, the tooling required to support BEL and the infrastructure hosting the OpenBEL resources.

BEL Statement

A BEL Statement is an expression that represents knowledge of the existence of biological entities and relationships between them that are known to be observed within a particular experiment context (i.e. Experiment Context), based on some source of prior knowledge such as a scientific publication or newly generated experimental data.

Namespace

A set of biological identifiers that are curated and maintained by an organization. An example of a namespace is the Gene Ontology or HGNC database. These biological identifiers are referenced within a BEL Statement.

Examples: p(HGNC:AKT1) => bp(GO:"apoptotic process")

  • References the AKT1 gene symbol from the HGNC database.
  • References the apoptotic process process term from the GO database.

Annotation

A name/value property that expresses knowledge about an aspect of a BEL Nanopub. You can apply an annotation to the Experiment Context or Metadata of a BEL Nanopub.

Examples: Given the BEL Statement p(HGNC:XRCC5,pmod(R)) => cat(p(HGNC:WRN))

  • We can apply an Ncbi Taxonomy annotation value of Homo sapiens to the Experiment Context section of the BEL Nanopub.
  • We can apply a Curation Method annotation value of Text Mining to the Metadata section of the BEL Nanopub.

BEL Nanopub

A Nanopub is defined by nanopub.org. Quoting their definition:

A nanopublication is the smallest unit of publishable information: an assertion about anything that can be uniquely identified and attributed to its author.

Individual nanopublications can be cited by others and tracked for their impact on the community.

Nanopublications are a natural response to the explosion of high-quality contextual information that overwhelms the capacity of conventional research articles in scholarly communication.

A BEL Nanopub is an atomic instance of BEL knowledge to represent a biological interaction or fact with an experimental context and provenance. A BEL Nanopub consists of the following parts:

  • Citation
    • The identification for the scientific literature where the interaction was stated.
  • BEL Statement
    • The biological interaction curated from the Citation.
  • Support
    • The section within the Citation that supports the BEL Statement. For example, this may be a text quotation, figure, or table within the Citation.
  • Experiment Context
    • The biological context within the experiment where the BEL Statement is observed. For example if the experiment sample was a biopsy on Human, Lung tissue then you might provide an Annotation of Ncbi Taxonomy with value Homo sapiens and Uberon with value lung epithelium.
  • Metadata
    • Additional data about the Nanopub itself. For example if the Nanopub was curated using a text mining approach we may provide a CurationMethod Annotation with value Text Mining.
  • References

Asserted BEL Nanopubs

BEL Nanopubs that are curated by the user and saved in the Nanopub Store are said to be asserted. Although they are created by the user there may be additional provenance associated within the BEL Nanopub.

Examples:

Derived BEL Nanopubs

BEL Nanopubs that can be reasoned from other BEL Nanopubs are said to be derived. These derivations are associated to the original BEL Nanopub with a description of the reasoning rules.

Example:

Note: The items here represent asserted and derived BEL Nanopubs. Here we only include the BEL statement for brevity.

Asserted

  • p(HGNC:TGFB1) increases deg(complex(SCOMP:"Nfkb Complex"))
    • An increase of the TGFB1 protein causes more of the Nfkb Complex complex to degrade.
  • Derived
    • deg(complex(SCOMP:"Nfkb Complex")) directlyDecreases complex(SCOMP:"Nfkb Complex")
      • The degradation of the Nfkb Complex directly causes a decrease in the abundance of Nfkb Complex.
    • p(MGI:Tgfb1) increases deg(complex(SCOMP:"Nfkb Complex"))
      • Because the mouse Tgfb1 protein is orthologous to human TGFB1 protein, it is expected to have a similar effect on the Nfkb Complex.

BKN - BEL Knowledge Network

Pronounced like 'beacon', this is a nodes and edges BEL network built from assembling Asserted BEL Nanopubs and Derived BEL Nanopubs. The BEL Statement triple of <Term> <Relationship> <Term> is represented as an edge with nodes for each <Term>.

The nodes and edges of a BKN can be Equivalenced and Orthologized. Review BEL RDF Model for a description of how equivalences are computed using the BEL RDF representation.

BEL Document

A file containing a collection of BEL Nanopubs with document metadata like Name, Description, and Version. The supported document formats are BEL script, XBEL, RDF, and BNJ - BEL Nanopub JSON file.

Dataset

The representation of a BEL Document within the OpenBEL API. This provides access to document metadata as well as the collection of BEL Nanopubs stored in the OpenBEL API that originate from the BEL Document.

Expression

A string encoded in BEL that may represent a parameter (e.g. AKT1, GO:"apoptotic process"), term (e.g. bp(GO:"apoptotic process")), or statement (e.g. p(HGNC:AKT1) increases bp(GO:"apoptotic process")).

BEL Nanopub Store

A database used to store BEL Nanopubs. It facilitates management of BEL Nanopubs and connection to other data sources.

BNJ - BEL Nanopub JSON file

BNJ (pronounced 'binge') is an array of BEL Nanopubs in JSON format. This is the most complete representation of a BEL Nanopub with associated metadata and includes namespace and annotation references. It is also the best format for importing and exporting BEL content from the OpenBEL API (BEL Nanopub Store).