bel ruby
The bel ruby gem allows the reading, writing, and processing of BEL (Biological Expression Language) with a natural DSL.
Learn more on BEL.
License: Apache License, Version 2.0
Dependencies
Required
- Ruby 2.0.0 or greater (how to install ruby)
Optional
- rdf gem, addressable gem, and uuid gem for RDF conversion
- rdf-turtle gem for serializing to RDF turtle format
Install / Build: See INSTALL.
A changelog is maintained at CHANGELOG.
branches
master branch
next branch
executable commands
bel: A single executable command with subcommands.
Usage: bel [OPTIONS]... COMMAND
A set of commands to process BEL knowledge.
Subcommands:
bel2rdf
compare
parse
rdfschema
summarize
translate
upgrade
bel 0.3.3
Copyright (C) 2015 OpenBEL
Apache License, Version 2.0, January 2004
http://www.apache.org/licenses/
Options:
-v, --verbose Verbose output.
-e, --version Print version and exit
-h, --help Show this message
bel2rdf.rb: Converts BEL to RDF.
# dumps RDF to standard out in ntriples format (default)
# (from file)
bel2rdf.rb --bel small_corpus.bel
# (from standard in)
cat small_corpus.bel | bel2rdf.rb
# dumps RDF to standard out in turtle format
# (from file)
bel2rdf.rb --bel small_corpus.bel --format turtle
# (from standard in)
cat small_corpus.bel | bel2rdf.rb --format turtle
bel_compare.rb: Compares knowledge in two BEL script files.
bel_compare.rb small_corpus.bel large_corpus.bel
bel_parse.rb: Show parsed objects from BEL content for debugging purposes
# ...from file
bel_parse.rb --bel small_corpus.bel
# ...from standard in
cat small_corpus.bel | bel_parse.rb
bel_rdfschema.rb: Dumps the RDF Schema triples for BEL.
# dumps schema in ntriples format (default)
bel_rdfschema.rb
# dumps schema in turtle format
# note: requires the 'rdf-turtle' gem
bel_rdfschema.rb --format turtle
bel_summarize.rb: Show summary statistics for knowledge in BEL script.
# using BEL file
bel_summarize.rb --bel small_corpus.bel
# using BEL from STDIN
cat small_corpus.bel | bel_summarize.rb
bel_upgrade.rb: Upgrade namespaces in BEL content to another version (i.e. 1.0 to 20131211)
# using BEL file and change log JSON file
bel_upgrade.rb --bel small_corpus.bel --changelog change_log.json
# using BEL file and change log from a URL
bel_upgrade.rb --bel small_corpus.bel --changelog http://resource.belframework.org/belframework/20131211/change_log.json
# using BEL from STDIN and change log from a URL
cat small_corpus.bel | bel_upgrade.rb --changelog http://resource.belframework.org/belframework/20131211/change_log.json
api examples
Use OpenBEL namespaces from the latest release.
require 'bel'
# reference namespace value using standard prefixes (HGNC, MGI, RGD, etc.)
HGNC['AKT1']
=> #<BEL::Model::Parameter:0x00000004df5bc0
@enc=:GRP,
@ns_def="BEL::Namespace::HGNC",
@value=:AKT1>
Load your own namespace
require 'bel'
# define a NamespaceDefinition with prefix symbol and url
PUBCHEM = NamespaceDefinition.new(:PUBCHEM, 'http://your-url.org/pubchem.belns')
# reference caffeine compound, sip, and enjoy
PUBCHEM['2519']
Load namespaces from a published OpenBEL version
require 'bel'
ResourceIndex.openbel_published_index('1.0').namespaces.find { |x| x.prefix == :HGU133P2 }
ResourceIndex.openbel_published_index('20131211').namespaces.find { |x| x.prefix == :AFFX }
ResourceIndex.openbel_published_index('latest-release').namespaces.find { |x| x.prefix == :AFFX }
Load namespaces from a custom resource index
require 'bel'
ResourceIndex.new('/home/bel/index.xml').namespaces.map(&:prefix)
=> ["AFFX", "CHEBIID", "CHEBI", "DOID", "DO", "EGID", "GOBPID", "GOBP",
"GOCCID", "GOCC", "HGNC", "MESHPP", "MESHCS", "MESHD", "MGI", "RGD",
"SCHEM", "SDIS", "SFAM", "SCOMP", "SPAC", "SP"]
Validate BEL parameters
require 'bel'
# AKT1 contained within HGNC NamespaceDefinition
HGNC[:AKT1].valid?
=> true
# not_in_namespace is not contained with HGNC NamespaceDefinition
HGNC[:not_in_namespace].valid?
=> false
# namespace is nil so :some_value MAY exist
Parameter.new(nil, :some_value).valid?
=> true
Validate BEL terms
require 'bel'
tscript(g(HGNC['AKT1'])).valid?
=> false
tscript(g(HGNC['AKT1'])).valid_signatures
=> []
tscript(g(HGNC['AKT1'])).invalid_signatures.map(&:to_s)
=> ["tscript(F:complex)a", "tscript(F:p)a"]
tscript(p(HGNC['AKT1'])).valid?
=> true
tscript(p(HGNC['AKT1'])).valid_signatures.map(&:to_s)
=> ["tscript(F:p)a"]
tscript(p(HGNC['AKT1'])).invalid_signatures.map(&:to_s)
=> ["tscript(F:complex)a"]
Write BEL in Ruby with a DSL
require 'bel'
# create BEL statements
p(HGNC['SKIL']).directlyDecreases tscript(p(HGNC['SMAD3']))
bp(GO['response to hypoxia']).increases tscript(p(EGID['7157']))
Parse BEL input
require 'bel'
# example BEL document
BEL_SCRIPT = <<-EOF
SET DOCUMENT Name = "Spec"
SET DOCUMENT Authors = User
SET Disease = "Atherosclerosis"
path(MESHD:Atherosclerosis)
path(Atherosclerosis)
bp(GO:"lipid oxidation")
p(MGI:Mapkap1) -> p(MGI:Akt1,pmod(P,S,473))
path(MESHD:Atherosclerosis) => bp(GO:"lipid oxidation")
path(MESHD:Atherosclerosis) =| (p(HGNC:MYC) -> bp(GO:"apoptotic process"))
EOF
# BEL::Script.parse returns BEL::Script::Parser
BEL::Script.parse('tscript(p(HGNC:AKT1))')
=> #<BEL::Script::Parser:0x007f179261d270>
# BEL::Script::Parser is Enumerable so we can analyze as we parse
# for example: count all function types into a hash
BEL::Script.parse('tscript(p(HGNC:AKT1))', {HGNC: HGNC}).find_all { |obj|
obj.is_a? Term
}.map { |term|
term.fx
}.reduce(Hash.new {|h,k| h[k] = 0}) { |result, function|
result[function.short_form] += 1
result
}
=> {:p=>1, :tscript=>1}
# parse; yield each parsed object to the block
namespace_mapping = {GO: GOBP, HGNC: HGNC, MGI: MGI, MESHD: MESHD}
BEL::Script.parse(BEL_SCRIPT, namespace_mapping) do |obj|
puts "#{obj.class} #{obj}"
end
=> BEL::Script::DocumentProperty: SET DOCUMENT Name = "Spec"
=> BEL::Script::DocumentProperty: SET DOCUMENT Authors = "User"
=> BEL::Script::Annotation: SET Disease = "Atherosclerosis"
=> BEL::Script::Parameter: MESHD:Atherosclerosis
=> BEL::Script::Term: path(MESHD:Atherosclerosis)
=> BEL::Script::Statement: path(MESHD:Atherosclerosis)
=> BEL::Script::Parameter: Atherosclerosis
=> BEL::Script::Term: path(Atherosclerosis)
=> BEL::Script::Statement: path(Atherosclerosis)
=> BEL::Script::Parameter: GO:"lipid oxidation"
=> BEL::Script::Term: bp(GO:"lipid oxidation")
=> BEL::Script::Statement: bp(GO:"lipid oxidation")
=> BEL::Script::Parameter: MGI:Mapkap1
=> BEL::Script::Term: p(MGI:Mapkap1)
=> BEL::Script::Parameter: MGI:Akt1
=> BEL::Script::Parameter: P
=> BEL::Script::Parameter: S
=> BEL::Script::Parameter: 473
=> BEL::Script::Term: p(MGI:Akt1,pmod(P,S,473))
=> BEL::Script::Statement: p(MGI:Mapkap1) -> p(MGI:Akt1,pmod(P,S,473))
=> BEL::Script::Parameter: MESHD:Atherosclerosis
=> BEL::Script::Term: path(MESHD:Atherosclerosis)
=> BEL::Script::Parameter: GO:"lipid oxidation"
=> BEL::Script::Term: bp(GO:"lipid oxidation")
=> BEL::Script::Statement: path(MESHD:Atherosclerosis) => bp(GO:"lipid oxidation")
=> BEL::Script::Parameter: MESHD:Atherosclerosis
=> BEL::Script::Term: path(MESHD:Atherosclerosis)
=> BEL::Script::Parameter: HGNC:MYC
=> BEL::Script::Term: p(HGNC:MYC)
=> BEL::Script::Parameter: GO:"apoptotic process"
=> BEL::Script::Term: bp(GO:"apoptotic process")
=> BEL::Script::Statement: path(MESHD:Atherosclerosis) =| (p(HGNC:MYC) -> bp(GO:"apoptotic process"))
Iteratively parse BEL from file-like object
require 'bel'
BEL::Script.parse(File.open('/home/user/small_corpus.bel')).find_all { |obj|
obj.is_a? Statement
}.to_a.size
Parse BEL and convert to RDF (requires the rdf, addressable, and uuid gems)
require 'bel'
parser = BEL::Script::Parser.new
rdf_statements = []
# parse term
parser.parse('p(HGNC:AKT1)') do |obj|
if obj.is_a? BEL::Model::Term
rdf_statements += obj.to_rdf
end
end
# parse statement
parser.parse("p(HGNC:AKT1) => tscript(g(HGNC:TNF))\n") do |obj|
if obj.is_a? BEL::Model::Statement
rdf_statements += obj.to_rdf
end
end