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The following is an example of a BEL Script document created from a PubMed abstract.

Additional BEL Script examples can be found here.

##############################################################################
#                                                                           
#
# Example BEL Script.                                                       
#
#                                                                            
# This BEL Script encodes BEL Statements extracted from PubMed ID 11340296   #
#                                                                           
#
##############################################################################

 
##############################################################################
#
# Properties Section
# This section is used to define properties associated with the document as a 
# whole.
#
# Set the Citation for the Document. This is generally used to define who
# created the document.

SET DOCUMENT Name = "Example BEL Script Document"

SET DOCUMENT Authors = "Selventa"

SET DOCUMENT Version = "1.0"

SET DOCUMENT Copyright = "Copyright (c) 2011, Selventa. All Rights Reserved"

# Set additional information for the Document. This is generally used to define why
# the document was created and what it can be used for.

SET DOCUMENT Description = "This document provides an illustration of the structure 
of a BEL Script document and the encoding of BEL Statements"

##############################################################################
#
# Definitions Section
# This section is used to define the Namespaces and Annotation Types that will 
# be used within the document.
#
# First define the Namespaces for term parameters. One Namespace can be set as 
# the DEFAULT Namespace for the document

DEFINE DEFAULT NAMESPACE HGNC AS URL \
 "http://resource.belframework.org/belframework/1.0/ns/hgnc-approved-\
 symbols.belns"

DEFINE NAMESPACE EGID AS URL \
 "http://resource.belframework.org/belframework/1.0/ns/entrez-gene-ids-hmr.belns"

# Next define Annotation Types to be used to annotate the BEL Statements that are 
# defined later on

# Here we set up a species annotation using the pre-defined species annotation type

# This species annotation uses NCBI TAX IDs

DEFINE ANNOTATION Species AS URL \
 "http://resource.belframework.org/belframework/1.0/annotation/species-taxonomy-id.belanno"

# Define a Tissues annotation type

DEFINE ANNOTATION Tissue AS URL \ 
 "http://resource.belframework.org/belframework/1.0/annotation/mesh-tissue.belanno"


# Define an ExposureTime Annotation Type using a REGEX pattern

DEFINE ANNOTATION ExposureTime AS PATTERN "[0-6]hr"

##############################################################################
#
# Statements Section
# This section is used to encode BEL Statements using the Namespaces and 
# Annotation Types previously defined.
#
# Set the citation for the PubMed article being used. The Citation and Evidence 
# Annotation types are part of the BEL specification and don't need to be defined as 
# Annotation Types
# Set the statement group. All following statements will be assigned to this group

SET STATEMENT_GROUP = "PubMed 11340296"

SET Citation = {"PubMed", "Exp Clin Immunogenet, 2001;18(2) 80-5", "11340296"}

# Set document-defined annotation values

SET Species = 9606

SET Tissue = "t-cells"

# Create an Evidence Line for a block of BEL Statements

SET Evidence = "Here we show that interfereon-alpha
 (IFNalpha) is a potent producer of SOCS expression in human T cells, as high expression of CIS, SOCS-1, SOCS-2, 
 and SOCS-3 was detectable after IFNalpha stimulation. After 4 h of stimulation CIS, SOCS-1, and SOCS-3 had returned to baseline
 levels, whereas SOCS-2 expression had not declined."

SET ExposureTime = "4hr"

# Create some BEL Statements. The following statements will be annotated with Citation,

# Species, Tissue, Evidence and ExposureTime annotation type values defined above.

p(HGNC:IFNA1) -> r(HGNC:CISH) // protein abundance of IFNA1 increases the rna \
      abundance of CISH

p(HGNC:IFNA1) -> r(HGNC:SOCS1) // protein abundance of IFNA1 increases the rna \
      abundance of SOCS1

p(HGNC:IFNA1) -> r(HGNC:SOCS2) // protein abundance of IFNA1 increases the rna \
      abundance of SOCS2

p(HGNC:IFNA1) -> r(HGNC:SOCS3) // protein abundance of IFNA1 increases the rna \
      abundance of SOCS3

# Reset the Evidence line and ExposureTime Annotation Type values

SET Evidence = "In contrast, after IL-2 induction neither CIS, SOCS-1, nor SOCS-2
 expression levels declined after 6h."

SET ExposureTime = "6hr"

# The following statements will be annotated with Citation, Species,
# Tissue, Evidence and ExposureTime annotation type values defined above.

p(HGNC:IL2) -> r(HGNC:CISH)       // protein abundance of IL2 increases the rna \
	abundance of CISH

p(HGNC:IL2) -> r(HGNC:SOCS1)      // protein abundance of IL2 increases the rna \
    abundance of SOSC1

p(HGNC:IL2) -> r(HGNC:SOCS2)      //protein abundance of IL2 increases the rna \
    abundance of SOSC2

 

 

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