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


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  1. #
  2. Example BEL Script. #
  3. #
  4. This BEL Script encodes BEL Statements extracted from PubMed ID 11340296 #
  5. #
    ##############################################################################

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    #
  6. Properties Section
  7. This section is used to define properties associated with the document as a
  8. whole.
    #
  9. Set the Citation for the Document. This is generally used to define who
  10. 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"
  11. Set additional information for the Document. This is generally used to define why
  12. 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"
    ##############################################################################
    #
  13. Definitions Section
  14. This section is used to define the Namespaces and Annotation Types that will
  15. be used within the document.
    #
  16. First define the Namespaces for term parameters. One Namespace can be set as
  17. 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"
  18. Next define Annotation Types to be used to annotate the BEL Statements that are
  19. defined later on
  20. Here we set up a species annotation using the pre-defined species annotation type
  21. This species annotation uses NCBI TAX IDs
    DEFINE ANNOTATION Species AS URL \"http://resource.belframework.org/belframework/1.0/annotation/species-taxonomy-id.belanno"
  22. Define a Tissues annotation type
    DEFINE ANNOTATION Tissue AS URL \"http://resource.belframework.org/belframework/1.0/annotation/mesh-sense-organ.belanno"
  23. Define an ExposureTime Annotation Type using a REGEX pattern
    DEFINE ANNOTATION ExposureTime AS PATTERN "[0-6]hr"
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    #
  24. Statements Section
  25. This section is used to encode BEL Statements using the Namespaces and
  26. Annotation Types previously defined.
    #
  27. Set the citation for the PubMed article being used. The Citation and Evidence
  28. Annotation types are part of the BEL specification and don't need to be defined as
  29. Annotation Types
  30. 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"}
  31. Set document-defined annotation values
    SET Species = 9606
    SET Tissue = "t-cells"
  32. 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"
  33. Create some BEL Statements. The following statements will be annotated with Citation,
  34. 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
  35. 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"
  36. The following statements will be annotated with Citation, Species,
  37. 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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