pybel-github-example/slushy.bel at master · bel-curation/pybel-github-example · GitHub

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SET DOCUMENT Name = "Worst. BEL Document. Ever."
SET DOCUMENT Description = "This document outlines all of the evil and awful work that is possible during BEL curation"
SET DOCUMENT Version = "0.0"
SET DOCUMENT Authors = "Charles Tapley Hoyt"
SET DOCUMENT Licenses = "WTF License"
# SET DOCUMENT ContactInfo = "charles.hoyt@scai.fraunhofer.de"  # Missing Contact Info is required
# SET DOCUMENT InvalidMetadata = "very invalid, indeed"

DEFINE NAMESPACE HGNC AS URL "https://owncloud.scai.fraunhofer.de/index.php/s/JsfpQvkdx3Y5EMx/download?path=hgnc-human-genes.belns"
DEFINE NAMESPACE GO AS URL "https://owncloud.scai.fraunhofer.de/index.php/s/JsfpQvkdx3Y5EMx/download?path=go-biological-process.belns"

DEFINE NAMESPACE dbSNP AS PATTERN "rs[0-9]+$"

DEFINE ANNOTATION CellLine AS URL "https://owncloud.scai.fraunhofer.de/index.php/s/JsfpQvkdx3Y5EMx/download?path=cell-line.belanno"
DEFINE ANNOTATION TextLocation AS LIST {"Abstract","Results","Legend","Review"}
DEFINE ANNOTATION Disease AS URL "https://owncloud.scai.fraunhofer.de/index.php/s/JsfpQvkdx3Y5EMx/download?path=mesh-diseases.belanno"

#: Name doesn't match annotation file Keyword (LexicographyWarning, not implemented yet)
DEFINE ANNOTATION Specieses AS  URL "https://owncloud.scai.fraunhofer.de/index.php/s/JsfpQvkdx3Y5EMx/download?path=species-taxonomy-id.belanno"

DEFINE ANNOTATION PowerLevel AS PATTERN "[0-9]+$"

# MissingAnnotationKeyWarning
UNSET STATEMENT_GROUP

# MissingAnnotationKeyWarning
UNSET Citation

SET STATEMENT_GROUP = "Group 1"

# InvalidCitationException
SET Citation = {"PubMed"}

# InvalidCitationType
SET Citation = {"Pubmed", "Incomplete", "1234"}

# InvalidPubMedIdentifierWarning
SET Citation = {"PubMed", "Fake Name", "Fake Reference"}

# MissingCitationException
p(HGNC:AKT1) -- p(HGNC:AKT2)

SET Citation = {"PubMed","Trends in molecular medicine","12928037"}

# MissingAnnotationKeyWarning
UNSET Evidence

# MissingAnnotationKeyWarning
UNSET PowerLevel

# MissingSupportWarning
p(HGNC:AKT1) -- p(HGNC:AKT2)

SET Evidence = "This is definitely real evidence"

# Naked name (NakedNameWarning)
biologicalProcess("response to oxidative stress") increases biologicalProcess(GO:necrosis)

# UndefinedNamespaceWarning
p(UNDEFINED:"YFG") -- p(HGNC:AKT1)

# Missing name (MissingNamespaceNameWarning)
biologicalProcess(GO:"maybe response to oxidative stress") increases biologicalProcess(GO:necrosis)

# UndefinedAnnotationWarning
SET UNDEFINED_ANNOTATION = "Nope."

# MissingAnnotationKeyWarning
UNSET TextLocation

# IllegalAnnotationValueWarning
SET TextLocation = "Nope"

# MissingAnnotationRegexWarning
SET PowerLevel = "Nine Thousand"

# MissingNamespaceRegexWarning
g(dbSNP:"rs123123-A") eq g(HGNC:TP53)

# MalformedTranslocationWarning
tloc(p(HGNC:AKT1)) -- p(HGNC:AKT2)

# PlaceholderAminoAcidWarning
p(HGNC:AKT1, sub(G, 1, X)) -- p(HGNC:AKT2)

# NestedRelationWarning
p(HGNC:AKT1) -> (p(HGNC:AKT2) -> biologicalProcess(GO:"response to oxidative stress"))

# InvalidFunctionSemantic
bp(HGNC:AKT1) -> p(HGNC:AKT2)

# Forgot quotes (ParseException)
# SET Disease = Atherosclerosis

# Mixed up arguments (ParseException)
p(HGNC:TP53,sub(Q,R,248)) directlyDecreases transcriptionalActivity(proteinAbundance(HGNC:TP53))

UNSET STATEMENT_GROUP

######## The following statements have no errors #############

SET STATEMENT_GROUP = "Group 2"

SET Citation = {"PubMed","That one article from last week","123455"}
SET Evidence = "Evidence 1"
p(HGNC:AKT1) -> p(HGNC:EGFR)