sylfy 0.0.2 → 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +2 -0
- data/Rakefile +13 -0
- data/lib/sylfy.rb +12 -25
- data/lib/sylfy/add.rb +10 -0
- data/lib/sylfy/add/bio_kegg_kgml.rb +108 -0
- data/lib/sylfy/datamodel.rb +141 -0
- data/lib/sylfy/feature.rb +128 -0
- data/lib/sylfy/mathf.rb +40 -0
- data/lib/sylfy/pattern.rb +14 -0
- data/lib/sylfy/service.rb +34 -0
- data/lib/sylfy/service/biocycrest.rb +41 -0
- data/lib/sylfy/service/cactusncirest.rb +64 -0
- data/lib/sylfy/service/cbioportal.rb +156 -0
- data/lib/sylfy/service/chembl.rb +106 -0
- data/lib/sylfy/service/ebisoap.rb +55 -0
- data/lib/sylfy/service/ensemblrest.rb +64 -0
- data/lib/sylfy/service/ensemblrest/archive.rb +35 -0
- data/lib/sylfy/service/ensemblrest/comparative.rb +146 -0
- data/lib/sylfy/service/ensemblrest/xrefs.rb +73 -0
- data/lib/sylfy/service/hgncrest.rb +52 -0
- data/lib/sylfy/service/keggrest.rb +6 -19
- data/lib/sylfy/service/keggrest/conv.rb +64 -40
- data/lib/sylfy/service/keggrest/find.rb +27 -48
- data/lib/sylfy/service/keggrest/get.rb +82 -0
- data/lib/sylfy/service/keggrest/link.rb +17 -37
- data/lib/sylfy/service/keggrest/list.rb +18 -50
- data/lib/sylfy/service/lipidmaprest.rb +228 -0
- data/lib/sylfy/service/pubchem.rb +71 -0
- data/lib/sylfy/service/pubchemrest.rb +249 -0
- data/lib/sylfy/service/rest.rb +26 -0
- data/lib/sylfy/service/soapwsdl.rb +78 -0
- data/lib/sylfy/service/unichemrest.rb +106 -0
- data/lib/sylfy/utils.rb +18 -0
- data/lib/sylfy/utils/keyhash.rb +1149 -0
- data/lib/sylfy/utils/reactionkey.rb +197 -0
- data/lib/sylfy/version.rb +1 -1
- data/sylfy.gemspec +11 -15
- data/test/test_kegg_rest.rb +58 -0
- data/test/test_reactionkey.rb +37 -0
- metadata +87 -15
- data/lib/sylfy/math.rb +0 -24
- data/lib/sylfy/service/keggrest/restKegg_get.rb +0 -130
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#
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# Systems biology library for Ruby (Sylfy)
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#
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# author: Natapol Pornputtapong <natapol@chalmers.se>
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#
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# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
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#
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# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
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require 'sylfy/service/soapwsdl'
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module Sylfy
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# A module supports as interfaces for web services
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module Service
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module ChEBI
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class SOAP < Sylfy::Service::SOAPWSDL
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def initialize(options = {})
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super('http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl', options)
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end
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end
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module_function
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# Search ChEBI database using InChI
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#
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# == Parameters:
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# inchi::
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# inchi string to search
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def idbyinchi(inchi)
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output = Sylfy::Service::ChEBI::SOAP.new.get_structure_search(structure: Rubabel[inchi, :inchi].to_s(:can), type: 'SMILES', structureSearchCategory: 'IDENTITY')
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return output != nil ? ["urn:miriam:chebi:#{output[:list_element][:chebi_id]}"] : []
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end
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end
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module Miriam
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class SOAP < Sylfy::Service::SOAPWSDL
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def initialize(options = {})
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super('http://www.ebi.ac.uk/miriamws/main/MiriamWebServices?wsdl', options)
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end
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end
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end
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end
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end
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#p Sylfy::Service::PubChem::REST.compound('QIQXTHQIDYTFRH-UHFFFAOYSA-N', :inchikey, 'xrefs/SBURL')["InformationList"]["Information"][0]["SBURL"]
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#p Sylfy::Service::ChEBI::SOAP.new().get_complete_entity(chebiId: "CHEBI:15377")
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#p Sylfy::Service::Miriam::SOAP.new().get_official_data_type_uri("nickname" => "ChEBI")
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#p Sylfy::Service::Miriam::SOAP.new().convert_url(string: "urn:miriam:chebi:CHEBI:28842")
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#p Sylfy::Service::Miriam::SOAP.new().get_official_data_type_uri(nickname: "chebi")
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#p Sylfy::Service::Miriam::SOAP.new().get_miriam_uri(uri: "http://www.ebi.ac.uk/chebi/#CHEBI:17891")
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# @author Natapol Pornputtapong <natapol@chalmers.se>
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#
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require 'open-uri'
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require 'net/http'
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require 'rexml/document'
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require 'json'
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require 'yaml'
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require 'sylfy/service/ensemblrest/xrefs.rb'
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require 'sylfy/service/ensemblrest/archive.rb'
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require 'sylfy/service/ensemblrest/comparative.rb'
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module Sylfy
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module Service
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module ENSEMBL
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module REST
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BASEURI = URI.parse("http://beta.rest.ensembl.org")
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HTTP = Net::HTTP.new(BASEURI.host, BASEURI.port)
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module_function
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# internal method supporting all ENSEMBLREST service
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#
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# @param get_path [String] service get_path
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#
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# @param option_type [Array] list of option type of service
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def service(get_path, option_type = [], option={})
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optionList = []
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option.each do |k, v|
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optionList.push("#{k}=#{v}") if option_type.include?(k.to_sym)
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end
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get_path += "?#{optionList.join(";")}" if !optionList.empty?
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request = Net::HTTP::Get.new(get_path, {'Content-Type' => option.has_key?('content-type') ? option['content-type'] : 'application/json'})
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response = HTTP.request(request)
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if response.code != "200"
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#raise ParameterError, "Invalid response: #{response.code}"
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else
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if option.has_key?('content-type') && option['content-type'] != 'application/json'
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return response.body
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else
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return JSON.parse(response.body)
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end
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end
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end
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end
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end
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end
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end
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# @author Natapol Pornputtapong <natapol@chalmers.se>
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#
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require 'json'
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module Sylfy
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module Service
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module ENSEMBLREST
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module REST
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module Archive
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SERVICENAME = 'archive'
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module_function
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# Uses the given identifier to return the archived sequence
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#
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# @param id [String] The stable identifier of the entity you wish to retrieve overlapping features
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/archive_id}
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#
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# @return [array of Hash] results
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#
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def id(id, option = {})
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option_type = [:callback]
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get_path = "/#{SERVICENAME}/id/#{id}"
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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end
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end
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end
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end
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end
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# @author Natapol Pornputtapong <natapol@chalmers.se>
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#
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require 'json'
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module Sylfy
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module Service
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module ENSEMBL
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module REST
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module Alignment
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SERVICENAME = 'alignment'
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module_function
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# Retrieves genomic alignments as separate blocks based on its location
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#
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# @param species [String] Registry name/aliases used to restrict searches by
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#
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# @param region [String] The region to retrieve sequence for. A maximum of
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# 10Mb is allowed to be requested at any one time
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def block(species, region, option = {})
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option_type = [:callback, :compact, :compara, :display_species_set, :mask, :method, :species_set, :species_set_group]
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get_path = "/#{SERVICENAME}/block/region/#{species}/#{region}"
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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# Retrieves genomic alignments as a single slice based on its location
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#
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# @param species [String] Registry name/aliases used to restrict searches by
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#
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# @param region [String] The region to retrieve sequence for. A maximum of
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# 10Mb is allowed to be requested at any one time
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def slice(species, region, option = {})
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option_type = [:callback, :compact, :compara, :display_species_set, :expanded, :mask, :method, :overlap, :species_set, :species_set_group]
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get_path = "/#{SERVICENAME}/slice/region/#{species}/#{region}"
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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end
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module Genetree
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SERVICENAME = 'genetree'
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module_function
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# Retrieves Gene Tree dumps for a given Gene Tree stable identifier
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#
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# @param id [String] Ensembl GeneTree ID
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def id(id, option = {})
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option_type = [:aligned, :nh_format , :sequence]
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get_path = "/#{SERVICENAME}/id/#{id}"
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option['Content-Type'] = 'text/x-nh'
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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# Retrieves the Gene Tree that contains the given stable identifier
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#
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# @param id [String] Ensembl gene ID
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def member(id, option = {})
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option_type = [:db_type, :object_type , :species]
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get_path = "/#{SERVICENAME}/member/id/#{id}"
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option['Content-Type'] = 'text/x-phyloxml+xml'
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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# Retrieves a Gene Tree containing the Gene identified by the given symbol
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#
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# @param species [String] Registry name/aliases used to restrict searches by
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#
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# @param symbol [String] The external name/symbol to search for
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def symbol(species, symbol, option = {})
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option_type = [:db_type, :external_db, :object_type]
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get_path = "/#{SERVICENAME}/member/symbol/#{species}/#{symbol}"
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option['Content-Type'] = 'text/x-phyloxml+xml'
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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end
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module Homology
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SERVICENAME = 'homology'
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module_function
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# Retrieves homology information by ensembl gene id
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#
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# @param id [String] Ensembl GeneTree ID
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def id(id, option = {})
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option_type = [:aligned, :callback, :format, :sequence, :species, :target_species, :target_taxon, :type]
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get_path = "/#{SERVICENAME}/id/#{id}"
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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# Retrieves homology information by symbol
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#
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# @param species [String] Registry name/aliases used to restrict searches by
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#
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# @param symbol [String] The external name/symbol to search for
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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def symbol(species, symbol, option = {})
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option_type = [:aligned, :callback, :compara, :external_db, :format, :sequence, :target_species, :target_taxon, :type]
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get_path = "/#{SERVICENAME}/symbol/#{species}/#{symbol}"
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return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
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end
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end
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end
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end
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end
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end
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# @author Natapol Pornputtapong <natapol@chalmers.se>
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#
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require 'json'
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module Sylfy
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module Service
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module ENSEMBL
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module REST
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module Xrefs
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SERVICENAME = 'xrefs'
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module_function
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# Perform lookups of Ensembl Identifiers and retrieve their external cross references
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# in other databases
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#
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# @param id [String] ENSEMBL id
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#
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# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
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#
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# @return [array of Hash] results
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#
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+
def id(id, option = {})
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28
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+
option_type = [:all_levels, :callback, :db_type, :external_db, :object_type, :species]
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29
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+
get_path = "/#{SERVICENAME}/id/#{id}"
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30
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+
return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
|
31
|
+
end
|
32
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+
|
33
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+
# Performs a lookup based upon the primary accession or display label of an external
|
34
|
+
# reference and returning the information we hold about the entry
|
35
|
+
#
|
36
|
+
# @param species [String] Registry name/aliases used to restrict searches by
|
37
|
+
#
|
38
|
+
# @param name [String] The external name/primary accession to search for
|
39
|
+
#
|
40
|
+
# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
|
41
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+
#
|
42
|
+
# @return [array of Hash] results
|
43
|
+
#
|
44
|
+
def name(species, name, option = {})
|
45
|
+
option_type = [:callback, :db_type, :external_db]
|
46
|
+
get_path = "/#{SERVICENAME}/name/#{species}/#{name}"
|
47
|
+
return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
|
48
|
+
end
|
49
|
+
|
50
|
+
# Looks up an external symbol and returns all Ensembl objects linked to it.
|
51
|
+
# This can be a display name for a gene/transcript/translation, a synonym or an
|
52
|
+
# externally linked reference. If a Gene's transcript is linked to the supplied
|
53
|
+
# symbol the service will return both Gene and Transcript (it supports transient
|
54
|
+
# links).
|
55
|
+
#
|
56
|
+
# @param species [String] Registry name/aliases used to restrict searches by
|
57
|
+
#
|
58
|
+
# @param symbol [String] The external name/symbol to search for
|
59
|
+
#
|
60
|
+
# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
|
61
|
+
#
|
62
|
+
# @return [array of Hash] results
|
63
|
+
#
|
64
|
+
def symbol(species, symbol, option = {})
|
65
|
+
option_type = [:callback, :db_type, :external_db, :object_type]
|
66
|
+
get_path = "/#{SERVICENAME}/symbol/#{species}/#{symbol}"
|
67
|
+
return Sylfy::Service::ENSEMBLREST::service(get_path, option_type, option)
|
68
|
+
end
|
69
|
+
end
|
70
|
+
end
|
71
|
+
end
|
72
|
+
end
|
73
|
+
end
|
@@ -0,0 +1,52 @@
|
|
1
|
+
# @author Natapol Pornputtapong <natapol@chalmers.se>
|
2
|
+
#
|
3
|
+
require 'open-uri'
|
4
|
+
require 'net/http'
|
5
|
+
require 'rexml/document'
|
6
|
+
require 'json'
|
7
|
+
require 'yaml'
|
8
|
+
|
9
|
+
module Sylfy
|
10
|
+
|
11
|
+
module Service
|
12
|
+
|
13
|
+
module ENSEMBL
|
14
|
+
|
15
|
+
module REST
|
16
|
+
|
17
|
+
BASEURI = URI.parse('http://rest.genenames.org')
|
18
|
+
HTTP = Net::HTTP.new(BASEURI.host, BASEURI.port)
|
19
|
+
|
20
|
+
module_function
|
21
|
+
# internal method supporting all ENSEMBLREST service
|
22
|
+
#
|
23
|
+
# @param get_path [String] service get_path
|
24
|
+
#
|
25
|
+
# @param option_type [Array] list of option type of service
|
26
|
+
#
|
27
|
+
# @param option [String] option of service please consult {http://beta.rest.ensembl.org/documentation/info/xref_id}
|
28
|
+
#
|
29
|
+
# @return [array of Hash] results
|
30
|
+
#
|
31
|
+
def info()
|
32
|
+
request = Net::HTTP::Get.new(get_path, {'Content-Type' => option.has_key?('content-type') ? option['content-type'] : 'application/json'})
|
33
|
+
response = HTTP.request(request)
|
34
|
+
|
35
|
+
if response.code != "200"
|
36
|
+
#raise ParameterError, "Invalid response: #{response.code}"
|
37
|
+
else
|
38
|
+
#return YAML::dump(JSON.parse(response.body))
|
39
|
+
if option.has_key?('content-type') && option['content-type'] != 'application/json'
|
40
|
+
return response.body
|
41
|
+
else
|
42
|
+
return JSON.parse(response.body)
|
43
|
+
end
|
44
|
+
end
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
end
|
49
|
+
|
50
|
+
end
|
51
|
+
|
52
|
+
end
|
@@ -1,7 +1,3 @@
|
|
1
|
-
#
|
2
|
-
# UniSysDB library in Ruby
|
3
|
-
# Copyright (C) 2012
|
4
|
-
#
|
5
1
|
# @author Natapol Pornputtapong <natapol@chalmers.se>
|
6
2
|
#
|
7
3
|
require 'open-uri'
|
@@ -11,6 +7,7 @@ require 'rexml/document'
|
|
11
7
|
|
12
8
|
require 'sylfy/service/keggrest/conv'
|
13
9
|
require 'sylfy/service/keggrest/find'
|
10
|
+
require 'sylfy/service/keggrest/get'
|
14
11
|
require 'sylfy/service/keggrest/link'
|
15
12
|
require 'sylfy/service/keggrest/list'
|
16
13
|
|
@@ -18,16 +15,14 @@ module Sylfy
|
|
18
15
|
|
19
16
|
module Service
|
20
17
|
|
21
|
-
|
22
|
-
# http://
|
23
|
-
#
|
24
|
-
# <argument> = <database> | <dbentries>
|
25
|
-
|
18
|
+
# interface to KEGG API
|
19
|
+
# {http://www.kegg.jp/kegg/rest/keggapi.html}
|
20
|
+
# info | list | find | get | conv | link
|
26
21
|
module KEGGREST
|
27
22
|
|
28
|
-
|
23
|
+
BASEURI = "http://rest.kegg.jp"
|
29
24
|
|
30
|
-
|
25
|
+
DB = [:pathway, :brite, :module, :disease, :drug, :environ,
|
31
26
|
:ko, :genome, :compound, :glycan, :reaction, :rpair,
|
32
27
|
:rclass, :enzyme, :genomes, :genes, :ligand, :kegg, :organism]
|
33
28
|
|
@@ -39,12 +34,4 @@ module Sylfy
|
|
39
34
|
end
|
40
35
|
end
|
41
36
|
|
42
|
-
#require '../unisys.rb'
|
43
|
-
|
44
|
-
#p Unisys::Service::RESTKegg.list('hsa:10458+ece:Z5100')
|
45
|
-
#p Unisys::Service::RESTKegg.find(:genes, 'shiga+toxin')
|
46
|
-
#p Unisys::Service::RESTKegg.conv('hsa:10458+ece:Z5100','ncbi-gi')
|
47
|
-
#p Unisys::Service::RESTKegg.get(:G00092)
|
48
|
-
#Unisys::Service::RESTKegg.getSmallMolecule(:G00092)
|
49
|
-
#p Unisys::Service::RESTKegg.link('hsa:10458+ece:Z5100', 'pathway')
|
50
37
|
|