bio-chembl 0.1.1 → 0.1.2

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Files changed (4) hide show
  1. data/README.md +122 -10
  2. data/VERSION +1 -1
  3. data/bio-chembl.gemspec +1 -1
  4. metadata +13 -2
data/README.md CHANGED
@@ -4,31 +4,142 @@
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  [ChEMBL REST Web Service API](https://www.ebi.ac.uk/chembldb/ws) client, parser and container classes.
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- REST API Client
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+ REST API address
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  ```ruby
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- # Show a web service URI
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- BioChEMBL::REST::ChEMBL_URI.compound("CHEMBL1")
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+ BioChEMBL::REST::ChEMBL_URI.status
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+ #=> "http://www.ebi.ac.uk/chemblws/status/"
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+ BioChEMBL::REST::ChEMBL_URI.compounds("CHEMBL1")
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+ #=> "http://www.ebi.ac.uk/chemblws/compounds/CHEMBL1"
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+ BioChEMBL::REST::ChEMBL_URI.targets("CHEMBL2477")
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+ #=> "http://www.ebi.ac.uk/chemblws/targets/CHEMBL2477"
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+ BioChEMBL::REST::ChEMBL_URI.assays("CHEMBL1217643")
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+ #=> "http://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643"
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+ ```
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- # GET the XML data of the ChEMBL ID CHEMBL1
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+ Get data in XML
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+ ```ruby
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  api = BioChEMBL::REST.new
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- api.compound("CHEMBL1")
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+ compound = api.compounds("CHEMBL1")
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+ targst = api.targets("CHEMBL2477")
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+ assay = api.assays("CHEMBL1217643")
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  ```
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-
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- Parser and container
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-
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+ Check the server status
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+ ```ruby
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+ BioChEMBL::REST.up? #=> true/false
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+ ```
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+ REST API client, parser and container: BioChEMBL::Compound
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  ```ruby
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  cpd = BioChEMBL::Compound.find("CHEMBL1")
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  cpd.chemblId #=> "CHEMBL1"
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  cpd.slimes
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- ba = cpd.bioactivities
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-
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+ smiles = "CC(=O)CC(C1=C(O)c2ccccc2OC1=O)c3ccccc3"
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+ cpds = BioChEMBL::Compound.find_all_by_smiles(smiles)
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+ cpds = BioChEMBL::Compound.find_all_by_substructure(smiles)
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+ cpds = BioChEMBL::Compound.find_all_by_similarity(smiles + "/70")
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+
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+ cpd.bioactivities[0].parent_compound.chemblId #=> "CHEMBL1"
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+
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+ xml = BioChEMBL::REST.new.compounds("CHEMBL1")
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+ cpd = BioChEMBL::Compound.parse_xml(xml)
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+ ```
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+ REST API client, parser and container: BioChEMBL::Target
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+ ```ruby
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+ target = BioChEMBL::Target.find("CHEMBL1785")
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+ target.chemblId #=> "CHEMBL1785"
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+ target.targetType #=> "PROTEIN"
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+ target.geneNames #=> "EDNRB; ETRB"
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+
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+ BioChEMBL.to_array(target.geneNames) #=> ["EDNRB", "ETRB"]
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+ synonyms = BioChEMBL.to_array(target.synonyms)
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+ synosyms[0] #=> "Endothelin B receptor"
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+
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+ target = BioChEMBL::Target.find_by_uniprot("Q13936")
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+
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+ target.bioactivities[0].target.chemblId #=> "CHEMBL1785"
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+
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+ xml = BioChEMBL::REST.new.targets("CHEMBL1785")
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+ target = BioChEMBL::Target.parse_xml(xml)
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+ ```
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+ REST API client, parser and container: BioChEMBL::Assay
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+ ```ruby
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  assay = BioChEMBL::Assay.find("CHEMBL1217643")
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+ assay.chemblId #=> "CHEMBL1217643"
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+
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+ assay.bioactivities[0].assay.chemblId #=> "CHEMBL1217643"
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+ assay.bioactivities[0].target
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+ assay.bioactivities[0].parent_compound
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+
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+ xml = BioChEMBL::REST.new.assays("CHEMBL1217643")
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+ assay = BioChEMBL::Assay.parse_xml(xml)
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+ ```
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+
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+ Parser and container: BioChEMBL::Bioactivity
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+ ```ruby
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+ cpd.bioactivities[0].parent_compound.chemblId
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+ target.bioactivities[0].target.chemblId
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+ assay.bioactivities[0].assay.chemblId
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  assay.bioactivities[0].target
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  assay.bioactivities[0].parent_compound
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  ```
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+ Getting Started with Ruby
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+ ```ruby
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+ require 'bio-chembl'
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+ # 1. Use UniProt accession to get target details
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+ puts "
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+ # =========================================================
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+ # 1. Use UniProt accession to get target details
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+ # =========================================================
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+ "
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+
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+ accession = "Q00534"
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+ target = BioChEMBL::Target.find_by_uniprot(accession)
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+
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+ puts "Target description: #{target.description}"
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+ puts "Target CHEMBLID: #{target.chemblId}"
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+
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+
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+ # 2. Get all bioactivties for target CHEMBL_ID
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+ puts "
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+ # =========================================================
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+ # 2. Get all bioactivties for target CHEMBL_ID
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+ # =========================================================
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+ "
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+
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+ bioactivities = target.bioactivities
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+
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+ puts "Bioactivity count: #{bioactivities.size}"
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+ puts "Bioactivity count (IC50's): #{bioactivities.find_all {|x| x.bioactivity__type =~ /IC50/}.size}"
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+
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+
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+ # 3. Get compounds with high binding affinity (IC50 < 100)
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+ puts "
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+ # =========================================================
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+ # 3. Get compounds with high binding affinity (IC50 < 100)
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+ # =========================================================
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+ "
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+
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+ bioactivities.find_all {|x| x.bioactivity__type =~ /IC50/ and x.value.to_i < 100 }.each do |ba|
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+ compound = ba.parent_compound
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+ print "Compound CHEMBLID: #{compound.chemblId}"
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+ puts " #{compound.smiles}"
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+ end
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+
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+ # 4. Get assay details for Ki actvity types
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+ puts "
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+ # =========================================================
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+ # 4. Get assay details for Ki actvity types
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+ # =========================================================
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+ "
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+
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+ bioactivities.find_all {|x| x.bioactivity__type =~ /Ki/i }.each do |ba|
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+ assay = ba.assay
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+ print "Assay CHEMBLID: #{assay.chemblId}"
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+ puts " #{assay.assayDescription}"
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+ end
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+ ```
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  Note: this software is under active development!
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  ## Installation
@@ -57,6 +168,7 @@ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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  ## Todo list
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+ * BioChEMBL::Compound#image method to get the image in png.
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  * BioChEMBL::Target.find_by_refesq method.
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  * JSON output support (parser and address).
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  * ChEMBL RDF support.
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.1.1
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+ 0.1.2
data/bio-chembl.gemspec CHANGED
@@ -5,7 +5,7 @@
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  Gem::Specification.new do |s|
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  s.name = %q{bio-chembl}
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- s.version = "0.1.1"
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+ s.version = "0.1.2"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Mitsuteru Nakao"]
metadata CHANGED
@@ -1,12 +1,13 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-chembl
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  version: !ruby/object:Gem::Version
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+ hash: 31
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  prerelease: false
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  segments:
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  - 0
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  - 1
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- - 1
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- version: 0.1.1
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+ - 2
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+ version: 0.1.2
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  platform: ruby
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  authors:
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  - Mitsuteru Nakao
@@ -25,6 +26,7 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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+ hash: 3
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  segments:
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  - 0
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  version: "0"
@@ -38,6 +40,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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+ hash: 31
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  segments:
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  - 3
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  - 12
@@ -52,6 +55,7 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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+ hash: 23
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  segments:
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  - 1
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  - 0
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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+ hash: 49
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  segments:
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  - 1
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  - 8
@@ -82,6 +87,7 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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+ hash: 3
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  segments:
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  - 1
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  - 4
@@ -97,6 +103,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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+ hash: 31
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  segments:
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  - 3
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  - 12
@@ -111,6 +118,7 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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+ hash: 3
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  segments:
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  - 0
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  version: "0"
@@ -124,6 +132,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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+ hash: 9
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  segments:
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  - 1
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  - 5
@@ -188,6 +197,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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+ hash: 3
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  segments:
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  - 0
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  version: "0"
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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+ hash: 3
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  segments:
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  - 0
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  version: "0"