bio-chembl

ChEMBL classes: ChEMBL REST Web Service API client, parser and container classes. AcriveRecord classes for ChEMBL14 mysql dump.

REST API address

    BioChEMBL::REST::ChEMBL_URI.status
     #=> "https://www.ebi.ac.uk/chemblws/status/" 
    BioChEMBL::REST::ChEMBL_URI.compounds("CHEMBL1") 
     #=> "https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1"
    BioChEMBL::REST::ChEMBL_URI.targets("CHEMBL2477") 
     #=> "https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477"
    BioChEMBL::REST::ChEMBL_URI.assays("CHEMBL1217643") 
     #=> "https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643"

Get data in XML

    api = BioChEMBL::REST.new
    compound = api.compounds("CHEMBL1")
    targst   = api.targets("CHEMBL2477")
    assay    = api.assays("CHEMBL1217643")

Check the server status

   BioChEMBL::REST.up? #=> true/false

REST API client, parser and container: BioChEMBL::Compound

    cpd = BioChEMBL::Compound.find("CHEMBL1")
    cpd.chemblId #=> "CHEMBL1"
    cpd.slimes
   
    smiles = "CC(=O)CC(C1=C(O)c2ccccc2OC1=O)c3ccccc3"
    cpds = BioChEMBL::Compound.find_all_by_smiles(smiles)
    cpds = BioChEMBL::Compound.find_all_by_substructure(smiles)
    cpds = BioChEMBL::Compound.find_all_by_similarity(smiles + "/70")

    cpd.bioactivities[0].parent_compound.chemblId #=> "CHEMBL1"
    
    xml = BioChEMBL::REST.new.compounds("CHEMBL1") 
    cpd = BioChEMBL::Compound.parse_xml(xml)

REST API client, parser and container: BioChEMBL::Target

    target = BioChEMBL::Target.find("CHEMBL1785")
    target.chemblId #=> "CHEMBL1785"
    target.targetType #=> "PROTEIN"
    target.geneNames #=> "EDNRB; ETRB"
    
    BioChEMBL.to_array(target.geneNames) #=> ["EDNRB", "ETRB"]
    synonyms = BioChEMBL.to_array(target.synonyms)
    synosyms[0] #=> "Endothelin B receptor"

    target = BioChEMBL::Target.find_by_uniprot("Q13936")
    
    target.bioactivities[0].target.chemblId #=> "CHEMBL1785"
    
    xml = BioChEMBL::REST.new.targets("CHEMBL1785")     
    target = BioChEMBL::Target.parse_xml(xml)

REST API client, parser and container: BioChEMBL::Assay

    assay = BioChEMBL::Assay.find("CHEMBL1217643")
    assay.chemblId #=> "CHEMBL1217643"
    
    assay.bioactivities[0].assay.chemblId #=> "CHEMBL1217643"
    assay.bioactivities[0].target
    assay.bioactivities[0].parent_compound
    
    xml = BioChEMBL::REST.new.assays("CHEMBL1217643") 
    assay = BioChEMBL::Assay.parse_xml(xml)

Parser and container: BioChEMBL::Bioactivity

    cpd.bioactivities[0].parent_compound.chemblId
    target.bioactivities[0].target.chemblId
    assay.bioactivities[0].assay.chemblId
    assay.bioactivities[0].target
    assay.bioactivities[0].parent_compound

Getting Started with Ruby

    require 'bio-chembl'
    # 1. Use UniProt accession to get target details
    puts "
    # =========================================================
    # 1. Use UniProt accession to get target details
    # =========================================================
    "
    
  	accession = "Q00534"
  	target = BioChEMBL::Target.find_by_uniprot(accession)
  	
  	puts "Target description:  #{target.description}"
  	puts "Target CHEMBLID:     #{target.chemblId}"
  	
  
    # 2. Get all bioactivties for target CHEMBL_ID
    puts "
	# =========================================================
	# 2. Get all bioactivties for target CHEMBL_ID
	# =========================================================
	"

	bioactivities = target.bioactivities
	
	puts "Bioactivity count:           #{bioactivities.size}"
	puts "Bioactivity count (IC50's):  #{bioactivities.find_all {|x| x.bioactivity__type =~ /IC50/}.size}"


	# 3. Get compounds with high binding affinity (IC50 < 100)
	puts "
	# =========================================================
	# 3. Get compounds with high binding affinity (IC50 < 100)
	# =========================================================
	"

	bioactivities.find_all {|x| x.bioactivity__type =~ /IC50/ and x.value.to_i < 100 }.each do |ba|
	  compound = ba.parent_compound
	  print "Compound CHEMBLID: #{compound.chemblId}"
	  puts "  #{compound.smiles}"
	end
	
	# 4. Get assay details for Ki actvity types
	puts "
	# =========================================================
	# 4. Get assay details for Ki actvity types
	# =========================================================
	"
	
	bioactivities.find_all {|x| x.bioactivity__type =~ /Ki/i }.each do |ba|
	  assay = ba.assay
	  print "Assay CHEMBLID:  #{assay.chemblId}"
	  puts "  #{assay.assayDescription}"
	end

ActiveRecord classes.

	require 'bio-chembl/chembldb.rb'
	
	ActiveRecord::Base.establish_connection( {:adapter => 'mysql', 
    	                                      :host => 'localhost',
        	                                  :port => 3306,
            	                              :username => 'chembl', 
                	                          :password => '', 
                    	                      :socket => '/tmp/mysql.sock',
                        	                  :database => 'chembl_14'} )
                        	                  
  	accession = "Q00534"
	target = BioChEMBL::ChEMBLDB::Target.find_by_protein_accession(accession)
	puts "Target description:  #{target.description}"
	puts "Target CHEMBLID:     #{target.chembl_id}"
	
	# ChEMBL ID
	chembl_id = "CHEMBL1"
	chemblid = BioChEMBL::ChEMBLDB::ChemblIdLookup.find(chembl_id)
	chemblid.entity_type 
	compound = chemblid.entity
	
	# Compound
	compound = BioChEMBL::ChEMBLDB::Molecule.find_by_chembl_id(chembl_id)
	activities = compound.compound_records.map {|x| x.activities }.flatten
	
	# Target
	target = BioChEMBL::ChEMBLDB::Target.find_by_chembl_id(chembl_id)
	activities = target.assays.map {|x| x.activities }.flatten
	
	# Assay
	assay = BioChEMBL::ChEMBLDB::Assay.find_by_chembl_id(chembl_id)
	activities = assay.activities

Note: this software is under active development!

Installation

    gem install bio-chembl

Usage

    require 'bio-chembl'

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/nakao/bio-chembl

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Todo list

• BioChEMBL::Compound#image method to get the image in png.
• BioChEMBL::Target.find_by_refesq method.
• JSON output support (parser and address).
• ChEMBL RDF integration.
• Local REST API server with local ChEMBL database.
• Connect Bioactivity#reference to external IDs (PubMed ID/DOI/CiteXplore)
• More high level methods for the ActiveRecord classes

Cite

If you use this software, please cite one of

• BioRuby: bioinformatics software for the Ruby programming language
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Biogems.info

This Biogem is published at #bio-chembl

Copyright

Copyright (c) 2012 Mitsuteru Nakao. See LICENSE.txt for further details.