From ff5b9add94c1a9f7e21aa7a8d5de5d701d2d141b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Mon, 2 Apr 2012 16:56:52 +0200 Subject: E-MTAB-798_philippe.zip as single test --- test/toxbank-investigation-curl.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/toxbank-investigation-curl.rb b/test/toxbank-investigation-curl.rb index 1c6726c..5856a1a 100644 --- a/test/toxbank-investigation-curl.rb +++ b/test/toxbank-investigation-curl.rb @@ -24,7 +24,7 @@ class UploadTest < Test::Unit::TestCase def test_03_valid_zip_upload # upload - #["isa-tab-renamed.zip"].each do |f| + #["E-MTAB-798_philippe.zip"].each do |f| ["BII-I-1.zip","isa-tab-renamed.zip","E-MTAB-798_philippe.zip"].each do |f| file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f response = `curl -Lk -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{@@subjectid}" #{$toxbank_investigation[:uri]}`.chomp -- cgit v1.2.3 From 61e8f17c12f1560f81fa5cdc0d7ddb05d16f70cc Mon Sep 17 00:00:00 2001 From: rautenberg Date: Tue, 10 Apr 2012 17:53:11 +0200 Subject: add test for default policy xml template --- test/policy.rb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/test/policy.rb b/test/policy.rb index c69175d..11014be 100644 --- a/test/policy.rb +++ b/test/policy.rb @@ -84,10 +84,9 @@ class PolicyTest < Test::Unit::TestCase assert_equal GROUP_TYPE, policy.type end -=begin def test_06_load_xml_and_check_defaults policies = OpenTox::Policies.new() - xml = File.read(File.join(File.dirname(__FILE__), "../lib/templates/default_policy.xml")) + xml = policies.get_xml_template("default_policy") policies.load_xml(xml) # check user policy policy = policies.policies["policy_user"] @@ -116,6 +115,5 @@ class PolicyTest < Test::Unit::TestCase assert policy.subject.type == GROUP_TYPE assert policy.subject.value == GROUP_VALUE end -=end end -- cgit v1.2.3 From ee76d660c9c4b6fcb93b903117d8590cc5443312 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Fri, 13 Apr 2012 13:51:31 +0200 Subject: change fixed variables to globals in test.rb configuration file --- test/authorization.rb | 6 ------ test/compound.rb | 23 +++++++++++++---------- test/dataset.rb | 24 +++++++++++++++--------- test/policy.rb | 12 +++--------- test/setup.rb | 11 +++++++---- test/task.rb | 31 +++++++++++++++---------------- 6 files changed, 53 insertions(+), 54 deletions(-) diff --git a/test/authorization.rb b/test/authorization.rb index 1556187..f23fe02 100644 --- a/test/authorization.rb +++ b/test/authorization.rb @@ -1,12 +1,6 @@ require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") TEST_URI = "http://only_a_test/test/" + rand(1000000).to_s -unless defined? $aa[:uri] #overwrite turned off A&A server for testing - $aa[:uri] = "https://opensso.in-silico.ch" - @@subjectid = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) -end - -@@subjectid ||= OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) class TestOpenToxAuthorizationBasic < Test::Unit::TestCase diff --git a/test/compound.rb b/test/compound.rb index 7573f58..8480892 100644 --- a/test/compound.rb +++ b/test/compound.rb @@ -1,38 +1,41 @@ require 'test/unit' require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") -class CompoundTest < Test::Unit::TestCase +begin + @@service_uri = $compound[:uri] +rescue + puts "Configuration Error: $compound[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") + exit +end - def setup - @service_uri = "http://ot-dev.in-silico.ch/compound" - end +class CompoundTest < Test::Unit::TestCase def test_compound_from_smiles_0 - c = OpenTox::Compound.from_smiles @service_uri, "F[B-](F)(F)F.[Na+]" + c = OpenTox::Compound.from_smiles @@service_uri, "F[B-](F)(F)F.[Na+]" assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.to_inchi assert_equal "[Na+].F[B-](F)(F)F", c.to_smiles # still does not work on 64bit machines end def test_compound_from_smiles_1 - c = OpenTox::Compound.from_smiles @service_uri, "CC(=O)CC(C)C#N" + c = OpenTox::Compound.from_smiles @@service_uri, "CC(=O)CC(C)C#N" assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.to_inchi assert_equal "CC(CC(=O)C)C#N", c.to_smiles end def test_compound_from_name - c = OpenTox::Compound.from_name @service_uri, "Benzene" + c = OpenTox::Compound.from_name @@service_uri, "Benzene" assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.to_inchi assert_equal "c1ccccc1", c.to_smiles end def test_compound_from_smiles_2 - c = OpenTox::Compound.from_smiles @service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F" + c = OpenTox::Compound.from_smiles @@service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F" assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.to_inchi assert_equal "N#[N+]c1ccccc1.F[B-](F)(F)F", c.to_smiles end def test_compound_from_inchi - c = OpenTox::Compound.from_inchi @service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H" + c = OpenTox::Compound.from_inchi @@service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H" assert_equal "c1ccccc1", c.to_smiles end @@ -44,7 +47,7 @@ class CompoundTest < Test::Unit::TestCase =begin def test_match_hits - c = OpenTox::Compound.from_smiles @service_uri, "N=C=C1CCC(=F=FO)C1" + c = OpenTox::Compound.from_smiles @@service_uri, "N=C=C1CCC(=F=FO)C1" assert_equal ({"FF"=>2, "CC"=>10, "C"=>6, "C1CCCC1"=>10, "C=C"=>2}), c.match_hits(['CC','F=F','C','C=C','FF','C1CCCC1','OO']) end =end diff --git a/test/dataset.rb b/test/dataset.rb index 8730154..71629c6 100644 --- a/test/dataset.rb +++ b/test/dataset.rb @@ -4,23 +4,29 @@ DATASET = "http://ot-dev.in-silico.ch/dataset" DATA_DIR = File.join(File.dirname(__FILE__),"data") # TODO: add subjectids +begin + @@service_uri = $dataset[:uri] +rescue + puts "Configuration Error: $dataset[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") + exit +end class DatasetTest < Test::Unit::TestCase def test_all - datasets = OpenTox::Dataset.all DATASET, @@subjectid + datasets = OpenTox::Dataset.all @@service_uri, @@subjectid assert_equal OpenTox::Dataset, datasets.first.class end def test_create_empty - d = OpenTox::Dataset.create DATASET, @@subjectid + d = OpenTox::Dataset.create @@service_uri, @@subjectid assert_equal OpenTox::Dataset, d.class - assert_match /#{DATASET}/, d.uri.to_s + assert_match /#{@@service_uri}/, d.uri.to_s d.delete :subjectid => @@subjectid end def test_create_from_file - d = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid + d = OpenTox::Dataset.from_file @@service_uri, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid assert_equal OpenTox::Dataset, d.class assert_equal d.uri, d[RDF::XSD.anyURI] assert_equal "EPAFHM.mini", d.metadata[RDF::URI("http://purl.org/dc/elements/1.1/title")].first.to_s # DC.title is http://purl.org/dc/terms/title @@ -32,7 +38,7 @@ class DatasetTest < Test::Unit::TestCase end def test_from_yaml - @dataset = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid + @dataset = OpenTox::Dataset.from_file @@service_uri, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid assert_equal OpenTox::Dataset, @dataset.class assert_equal "hamster_carcinogenicity", @dataset[RDF::URI("http://purl.org/dc/elements/1.1/title")] hamster_carc? @@ -42,7 +48,7 @@ class DatasetTest < Test::Unit::TestCase =begin # TODO: fix (mime type??0 and add Egons example def test_sdf_with_multiple_features - @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf" + @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf" assert_equal OpenTox::Dataset, @dataset.class puts @dataset.features.size puts @dataset.compounds.size @@ -51,14 +57,14 @@ class DatasetTest < Test::Unit::TestCase =end def test_multicolumn_csv - @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/multicolumn.csv", @@subjectid + @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/multicolumn.csv", @@subjectid assert_equal 5, @dataset.features.size assert_equal 4, @dataset.compounds.size @dataset.delete :subjectid => @@subjectid end def test_from_csv - @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid + @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid assert_equal OpenTox::Dataset, @dataset.class hamster_carc? @dataset.delete :subjectid => @@subjectid @@ -66,7 +72,7 @@ class DatasetTest < Test::Unit::TestCase =begin def test_save - d = OpenTox::Dataset.create DATASET + d = OpenTox::Dataset.create @@service_uri d.metadata d.metadata[RDF::DC.title] = "test" d.save diff --git a/test/policy.rb b/test/policy.rb index 11014be..6babcc6 100644 --- a/test/policy.rb +++ b/test/policy.rb @@ -11,12 +11,6 @@ POLICY_NAME = "test_policy_#{rand(100000)}" RULE_NAME = "test_rule_#{rand(100000)}" SUBJECT_NAME = "test_subject_#{rand(100000)}" -AA ||= "https://opensso.in-silico.ch" -AA_USER = "guest" -AA_PASS = "guest" - -@@subjectid = OpenTox::Authorization.authenticate(AA_USER,AA_PASS) - class PolicyTest < Test::Unit::TestCase def test_01_class @@ -67,16 +61,16 @@ class PolicyTest < Test::Unit::TestCase def test_04_group_user policies = OpenTox::Policies.new() - policies.load_default_policy(AA_USER, TEST_URI, "member") + policies.load_default_policy($aa[:user], TEST_URI, "member") assert_equal "member", policies.policies["policy_group"].group - assert_equal AA_USER, policies.policies["policy_user"].user + assert_equal $aa[:user], policies.policies["policy_user"].user end def test_05_DN policies = OpenTox::Policies.new() policies.new_policy(POLICY_NAME) policy = policies.policies[policies.names[0]] - policy.set_ot_user(AA_USER) + policy.set_ot_user($aa[:user]) assert_equal USER_VALUE, policy.value assert_equal USER_TYPE, policy.type policy.set_ot_group(USER_GROUP) diff --git a/test/setup.rb b/test/setup.rb index c63a17c..b035a80 100644 --- a/test/setup.rb +++ b/test/setup.rb @@ -4,8 +4,11 @@ Bundler.require require 'opentox-client' require File.join(ENV["HOME"],".opentox","config","test.rb") -if defined? $aa - @@subjectid = OpenTox::Authorization.authenticate($aa[:user], $aa[:password]) -else - @@subjectid = "" +begin + AA = $aa[:uri] + @@subjectid = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) + raise if !OpenTox::Authorization.is_token_valid(@@subjectid) +rescue + puts "Configuration Error: $aa[:uri], $aa[:user] or $aa[:password] are not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") + exit end diff --git a/test/task.rb b/test/task.rb index c45704b..f368663 100644 --- a/test/task.rb +++ b/test/task.rb @@ -2,17 +2,17 @@ require 'test/unit' require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") #require "./validate-owl.rb" -TASK_SERVICE_URI = "http://ot-dev.in-silico.ch/task" -#TASK_SERVICE_URI = "http://ot-test.in-silico.ch/task" -#TASK_SERVICE_URI = "https://ambit.uni-plovdiv.bg:8443/ambit2/task" #not compatible +begin + @@service_uri = $task[:uri] +rescue + puts "Configuration Error: $task[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") + exit +end class TaskTest < Test::Unit::TestCase - -=begin -=end def test_all - all = OpenTox::Task.all(TASK_SERVICE_URI) + all = OpenTox::Task.all(@@service_uri) assert_equal Array, all.class t = all.last assert_equal OpenTox::Task, t.class @@ -20,23 +20,22 @@ class TaskTest < Test::Unit::TestCase end def test_create_and_complete - task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test" do + task = OpenTox::Task.create @@service_uri, :description => "test" do sleep 1 - TASK_SERVICE_URI + @@service_uri end assert task.running? assert_equal "Running", task.hasStatus task.wait assert task.completed? assert_equal "Completed", task.hasStatus - assert_equal TASK_SERVICE_URI, task.resultURI + assert_equal @@service_uri, task.resultURI end - def test_create_and_cancel - task = OpenTox::Task.create TASK_SERVICE_URI do + task = OpenTox::Task.create @@service_uri do sleep 2 - TASK_SERVICE_URI + @@service_uri end assert task.running? task.cancel @@ -44,7 +43,7 @@ class TaskTest < Test::Unit::TestCase end def test_create_and_fail - task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do + task = OpenTox::Task.create @@service_uri, :description => "test failure", :creator => "http://test.org/fake_creator" do sleep 1 raise "A runtime error occured" end @@ -56,7 +55,7 @@ class TaskTest < Test::Unit::TestCase end def test_create_and_fail_with_opentox_error - task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do + task = OpenTox::Task.create @@service_uri, :description => "test failure", :creator => "http://test.org/fake_creator" do sleep 1 raise OpenTox::Error.new 500, "An OpenTox::Error occured" end @@ -70,7 +69,7 @@ class TaskTest < Test::Unit::TestCase =begin # temporarily removed until uri checking from virtual machines has been fixed def test_wrong_result_uri - task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do + task = OpenTox::Task.create @@service_uri, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do sleep 1 "Asasadasd" end -- cgit v1.2.3 From 3647be0249667579baff9a94068b913fdaf50d54 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Fri, 13 Apr 2012 14:52:21 +0200 Subject: puts service URI for manual and nightly test --- test/compound.rb | 1 + test/dataset.rb | 1 + test/task.rb | 1 + 3 files changed, 3 insertions(+) diff --git a/test/compound.rb b/test/compound.rb index 8480892..e1167d8 100644 --- a/test/compound.rb +++ b/test/compound.rb @@ -3,6 +3,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") begin @@service_uri = $compound[:uri] + puts "Service URI is: #{@@service_uri}" rescue puts "Configuration Error: $compound[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") exit diff --git a/test/dataset.rb b/test/dataset.rb index 71629c6..54c9871 100644 --- a/test/dataset.rb +++ b/test/dataset.rb @@ -6,6 +6,7 @@ DATA_DIR = File.join(File.dirname(__FILE__),"data") begin @@service_uri = $dataset[:uri] + puts "Service URI is: #{@@service_uri}" rescue puts "Configuration Error: $dataset[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") exit diff --git a/test/task.rb b/test/task.rb index f368663..dd80c5b 100644 --- a/test/task.rb +++ b/test/task.rb @@ -4,6 +4,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") begin @@service_uri = $task[:uri] + puts "Service URI is: #{@@service_uri}" rescue puts "Configuration Error: $task[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb") exit -- cgit v1.2.3 From bb438372abd50e8e10d1e6229550bbc645e26418 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Fri, 13 Apr 2012 17:46:13 +0200 Subject: delete investigation after tests --- test/toxbank-investigation-rest.rb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/test/toxbank-investigation-rest.rb b/test/toxbank-investigation-rest.rb index 8849d60..3e1b295 100644 --- a/test/toxbank-investigation-rest.rb +++ b/test/toxbank-investigation-rest.rb @@ -78,15 +78,12 @@ class BasicTestCRUDInvestigation < Test::Unit::TestCase assert response.index(@@uri.to_s) != nil, "URI: #{@@uri} is not in uri-list" end -=begin # delete investigation/{id} def test_99_delete_investigation result = OpenTox::RestClientWrapper.delete @@uri.to_s, {}, :subjectid => @@subjectid - assert_raise OpenTox::NotFoundError do - OpenTox::RestClientWrapper.get @@uri.to_s, {}, {:accept => "text/uri-list", :subjectid => @@subjectid} - end + assert result.match(/^Investigation [\d]+ deleted$/) + assert !OpenTox::Authorization.uri_has_policy(@@uri.to_s, @@subjectid) end -=end end -- cgit v1.2.3 From da91f344082075fde4afe2db89786aba645fe2c7 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Mon, 16 Apr 2012 11:07:52 +0200 Subject: adapt tests: deleted investigations have no policies --- test/toxbank-investigation-curl.rb | 2 ++ test/toxbank-investigation-xls.rb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/test/toxbank-investigation-curl.rb b/test/toxbank-investigation-curl.rb index 1c6726c..04487fd 100644 --- a/test/toxbank-investigation-curl.rb +++ b/test/toxbank-investigation-curl.rb @@ -54,6 +54,8 @@ class UploadTest < Test::Unit::TestCase response = `curl -Lk -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}` assert_match /200/, response response = `curl -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}` + assert_match /401/, response + response = `curl -I -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}` assert_match /404/, response end end diff --git a/test/toxbank-investigation-xls.rb b/test/toxbank-investigation-xls.rb index 492d990..9ce8b2a 100644 --- a/test/toxbank-investigation-xls.rb +++ b/test/toxbank-investigation-xls.rb @@ -56,6 +56,8 @@ class UploadTest < Test::Unit::TestCase response = `curl -Lk -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}` assert_match /200/, response response = `curl -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}` + assert_match /401/, response + response = `curl -I -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}` assert_match /404/, response end -- cgit v1.2.3 From e4d0118c50542e0c52356c60a829b6a46f204865 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 19 Apr 2012 18:07:06 +0200 Subject: inspect rdf content --- test/rdf_check.rb | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 test/rdf_check.rb diff --git a/test/rdf_check.rb b/test/rdf_check.rb new file mode 100644 index 0000000..a321154 --- /dev/null +++ b/test/rdf_check.rb @@ -0,0 +1,35 @@ +require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") + +class UploadTest < Test::Unit::TestCase + + def setup + end + + def teardown + end + + def test_01_query_sparqle_rdf + id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) + #test_all + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/`.chomp + assert_match /DoseResponse-Trial/, response + assert_match /Investigation/, response + assert_match /BII-I-1/, response + #test_id_query_sparqle + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /TB-DoseResponseTrial-acetaminophen/, response + #test_metadata_query_sparqle + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/metadata`.chomp + assert_match /DoseResponse-Trial/, response + #test_resource_ISA_Investigation + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/ISA_1879`.chomp + assert_match /[Person, User, Contact]/, response + #test_resource_Study + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/S1887`.chomp + assert_match /A451/, response + #test_resource_Assay + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/A451`.chomp + assert_match /Assay/, response + end + +end -- cgit v1.2.3 From 244dc8b268403b7fc265c317ff294e488ff55218 Mon Sep 17 00:00:00 2001 From: gebele Date: Fri, 20 Apr 2012 09:26:04 +0200 Subject: more content/resources --- test/rdf_check.rb | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/test/rdf_check.rb b/test/rdf_check.rb index a321154..58eecf1 100644 --- a/test/rdf_check.rb +++ b/test/rdf_check.rb @@ -8,28 +8,32 @@ class UploadTest < Test::Unit::TestCase def teardown end - def test_01_query_sparqle_rdf + def test_01_query_sparqle_rdf_BII_I_1 id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) #test_all response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/`.chomp - assert_match /DoseResponse-Trial/, response - assert_match /Investigation/, response - assert_match /BII-I-1/, response + assert_match /[https\:\/\/toxbanktest2, https\:\/\/toxbank\-dev]/, response #test_id_query_sparqle response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /TB-DoseResponseTrial-acetaminophen/, response + assert_match /[title, Manchester, givenname, Castrillo]/, response #test_metadata_query_sparqle response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/metadata`.chomp - assert_match /DoseResponse-Trial/, response - #test_resource_ISA_Investigation - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/ISA_1879`.chomp - assert_match /[Person, User, Contact]/, response + assert_match /[I2225, BII\-I\-1, S2223, S2224, Growth, Background]/, response + #test_resource_Investigation + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/I2225`.chomp + assert_match /[BII\-I\-1, title, Growth, abstract, Background]/, response #test_resource_Study - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/S1887`.chomp - assert_match /A451/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/S2223`.chomp + assert_match /[hasProtocol, P\_2202, description, Comprehensive, title, rapamycin, Rapamycin, Affymetrix]/, response #test_resource_Assay - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/A451`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/A1269`.chomp assert_match /Assay/, response + #test_resource_Protocol + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/P_2202`.chomp + assert_match /[mRNA, extraction]/, response + #test_resource_ISA + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/ISA_3981`.chomp + assert_match /[givenname, Castrillo, family\_name, Juan]/, response end end -- cgit v1.2.3 From 1fa53ac290b5314ba21b9004b517a89bad0e9366 Mon Sep 17 00:00:00 2001 From: gebele Date: Fri, 20 Apr 2012 10:32:17 +0200 Subject: test E_MTAB --- test/rdf_check.rb | 39 +++++++++++++++++++++++++++++++++++---- 1 file changed, 35 insertions(+), 4 deletions(-) diff --git a/test/rdf_check.rb b/test/rdf_check.rb index 58eecf1..82e1554 100644 --- a/test/rdf_check.rb +++ b/test/rdf_check.rb @@ -16,6 +16,9 @@ class UploadTest < Test::Unit::TestCase #test_id_query_sparqle response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[title, Manchester, givenname, Castrillo]/, response + #test_resource_ISA + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/ISA_3981`.chomp + assert_match /[givenname, Castrillo, family\_name, Juan]/, response #test_metadata_query_sparqle response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/metadata`.chomp assert_match /[I2225, BII\-I\-1, S2223, S2224, Growth, Background]/, response @@ -24,16 +27,44 @@ class UploadTest < Test::Unit::TestCase assert_match /[BII\-I\-1, title, Growth, abstract, Background]/, response #test_resource_Study response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/S2223`.chomp - assert_match /[hasProtocol, P\_2202, description, Comprehensive, title, rapamycin, Rapamycin, Affymetrix]/, response + assert_match /[hasAssay, A1269, hasProtocol, P\_2202, description, Comprehensive, title, rapamycin, Rapamycin, Affymetrix]/, response #test_resource_Assay response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/A1269`.chomp + #TODO fix Assay content assert_match /Assay/, response #test_resource_Protocol response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/P_2202`.chomp assert_match /[mRNA, extraction]/, response + end + def test_02_query_sparqle_rdf_E_MTAB + id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) + #test_all + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/`.chomp + assert_match /[https\:\/\/toxbanktest2, https\:\/\/toxbank\-dev]/, response + #test_id_query_sparqle + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + #TODO fix givenname + assert_match /[title, EMBL\-EBI, hasStudy, S2008, hasMember, ISA_60553]/, response #test_resource_ISA - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/ISA_3981`.chomp - assert_match /[givenname, Castrillo, family\_name, Juan]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/ISA_60553`.chomp + assert_match /[givenname, Ruth, family\_name, Akhtar]/, response + #test_metadata_query_sparqle + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/metadata`.chomp + assert_match /[I2]/, response + #test_resource_Investigation + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/I2`.chomp + #TODO assert_match /[title, abstract]/, response + assert_match /[S2008]/, response + #test_resource_Study + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/S2008`.chomp + assert_match /[TG\-GATEs]/, response + assert_match /[hasAssay, A1838, hasProtocol, P_2010]/, response + #test_resource_Assay + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/A1838`.chomp + #TODO fix Assay content + assert_match /Assay/, response + #test_resource_Protocol + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/P_2010`.chomp + assert_match /[label, P\-MTAB\-23090]/, response end - end -- cgit v1.2.3 From 894674a238e2c00c72674e6077282cbccff00472 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 25 Apr 2012 13:56:30 +0200 Subject: tests for feature service added --- test/feature.rb | 140 ++++++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 127 insertions(+), 13 deletions(-) diff --git a/test/feature.rb b/test/feature.rb index f6ce128..bf49bea 100644 --- a/test/feature.rb +++ b/test/feature.rb @@ -1,27 +1,142 @@ require 'test/unit' require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") -class FeatureTest < Test::Unit::TestCase +class FeatureRestTest < Test::Unit::TestCase - def setup - @features = [ - #@@classification_training_dataset.features.keys.first, - "http://apps.ideaconsult.net:8080/ambit2/feature/35796", - #File.join(OpenTox::Model::Lazar.all.last,"predicted","value") + def serialize rdf, format + string = RDF::Writer.for(format).buffer do |writer| + rdf.each{|statement| writer << statement} + end + string + end + + def parse string, format + rdf = RDF::Graph.new + RDF::Reader.for(format).new(string) do |reader| + reader.each_statement { |statement| rdf << statement } + end + rdf + end + # TODO: test supported accept/content-type formats + # TODO: test invalid rdfs + def test_01_create_feature + @@rdf = RDF::Graph.new + subject = RDF::Node.new + #subject = RDF::URI.new File.join($feature[:uri]), SecureRandom.uuid) + @@rdf << RDF::Statement.new(subject, RDF::DC.title, "test" ) + @@rdf << RDF::Statement.new(subject, RDF.type, RDF::OT.Feature) + + @@formats = [ + [:ntriples, "text/plain"], + [:rdfxml, "application/rdf+xml"], + [:turtle, 'text/turtle'] ] + @@uris = [] + + @@formats.each do |f| + @@uris << OpenTox::RestClientWrapper.post($feature[:uri], serialize(@@rdf, f[0]), :content_type => f[1]).chomp + assert_equal true, URI.accessible?(@@uris.last) + end + end + + def test_02_list_features + r = OpenTox::RestClientWrapper.get($feature[:uri], {}, :accept => "text/uri-list")#.split("\n") + @@uris.each{ |uri| assert_equal true, r.include?(uri) } + @@formats.each do |f| + rdf = OpenTox::RestClientWrapper.get($feature[:uri], {}, :accept => f[1]) + @@uris.each do |uri| + assert_match /#{uri}/, rdf + assert_match /test/, rdf + assert_match /Feature/, rdf + end + end + end + + def test_03_get_feature + @@uris.each do |uri| + @@formats.each do |f| + rdf = OpenTox::RestClientWrapper.get(uri, {}, :accept => f[1]) + # TODO compare with rdf serialization + assert_match /#{uri}/, rdf + end + end + end + + def test_04_add_to_feature + uri = @@uris.first + new_rdf = RDF::Graph.new + new_rdf << RDF::Statement.new(RDF::Node.new, RDF::DC.author, "XYZ") + @@formats.each do |f| + OpenTox::RestClientWrapper.post(uri, serialize(new_rdf,f[0]), :content_type => f[1]) + assert_match /XYZ/, OpenTox::RestClientWrapper.get(uri,{},:accept => f[1]) + # TODO compare with rdf serialization + end + end + + def test_05_replace_feature + @@formats.each do |f| + @@uris.each do |uri| + OpenTox::RestClientWrapper.put(uri, serialize(@@rdf,f[0]), :content_type => f[1]) + assert_equal true, URI.accessible?(uri) + assert_no_match /XYZ/, OpenTox::RestClientWrapper.get(uri,{},:accept => f[1]) + end + end end - def test_feature - @features.each do |uri| - f = OpenTox::Feature.new(uri) - assert_equal RDF::OT1.TUM_CDK_nAtom, f[RDF::OWL.sameAs] - assert_equal RDF::OT1.TUM_CDK_nAtom, f.metadata[RDF::OWL.sameAs].first.to_s - assert_equal [RDF::OT1.Feature,RDF::OT1.NumericFeature].sort, f[RDF.type].sort + def test_06_delete_feature + @@uris.each do |uri| + OpenTox::RestClientWrapper.delete(uri) + assert_raise OpenTox::RestCallError do + OpenTox::RestClientWrapper.get(uri) + end end end +end + =begin +class FeatureCrudTest < Test::Unit::TestCase + + def test_01_create_feature + @@feature = OpenTox::Feature.create $feature[:uri] + assert_equal true, URI.accessible?(@@feature.uri) + end + + def test_02_list_features + r = OpenTox::Feature.all($feature[:uri]) + assert_equal true, r.include?(@@feature) + end + + def test_03_get_feature + @@rdf = @@feature.metadata + assert_match /#{@@feature.uri}/, @@rdf + end + + def test_04_update_feature + @@feature[RDF::DC.title] = "test" + @@feature.save + assert_match "test", OpenTox::RestClientWrapper.get(@@uri) + end + + def test_05_delete_feature + uri = @@feature.uri + @@feature.delete + r = OpenTox::RestClientWrapper.get($feature[:uri]).split("\n") + assert_equal false, r.include?(@@uri) + assert_equal false, URI.accessible?(@@uri) + end + +end + + + def test_ambit_feature + uri = "http://apps.ideaconsult.net:8080/ambit2/feature/35796", + f = OpenTox::Feature.new(uri) + assert_equal RDF::OT1.TUM_CDK_nAtom, f[RDF::OWL.sameAs] + assert_equal RDF::OT1.TUM_CDK_nAtom, f.metadata[RDF::OWL.sameAs].first.to_s + assert_equal [RDF::OT1.Feature,RDF::OT1.NumericFeature].sort, f[RDF.type].sort + end def test_owl #@features.each do |uri| validate_owl @features.first, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/) @@ -32,4 +147,3 @@ class FeatureTest < Test::Unit::TestCase =end -end -- cgit v1.2.3 From 9ee6c46003a1cf9c6f61e23d122013998d49baa6 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 3 May 2012 17:17:14 +0200 Subject: tests rdf content with TB specific fields --- test/rdf_check.rb | 79 ++++++++++++++++++++----------------------------------- 1 file changed, 28 insertions(+), 51 deletions(-) diff --git a/test/rdf_check.rb b/test/rdf_check.rb index 82e1554..587e342 100644 --- a/test/rdf_check.rb +++ b/test/rdf_check.rb @@ -8,63 +8,40 @@ class UploadTest < Test::Unit::TestCase def teardown end - def test_01_query_sparqle_rdf_BII_I_1 + def test_01_check_rdf_with_ToxBank_specific_fields_on_BII_I_1 id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - #test_all - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/`.chomp - assert_match /[https\:\/\/toxbanktest2, https\:\/\/toxbank\-dev]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Investigation Identifier, BII\-I\-1]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Owning Organisation URI, TBO\:G176]/, response #test_id_query_sparqle response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[title, Manchester, givenname, Castrillo]/, response + assert_match /[Consortium URI, TBC:G2]/, response #test_resource_ISA - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/ISA_3981`.chomp - assert_match /[givenname, Castrillo, family\_name, Juan]/, response - #test_metadata_query_sparqle - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/metadata`.chomp - assert_match /[I2225, BII\-I\-1, S2223, S2224, Growth, Background]/, response - #test_resource_Investigation - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/I2225`.chomp - assert_match /[BII\-I\-1, title, Growth, abstract, Background]/, response - #test_resource_Study - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/S2223`.chomp - assert_match /[hasAssay, A1269, hasProtocol, P\_2202, description, Comprehensive, title, rapamycin, Rapamycin, Affymetrix]/, response - #test_resource_Assay - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/A1269`.chomp - #TODO fix Assay content - assert_match /Assay/, response - #test_resource_Protocol - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0/P_2202`.chomp - assert_match /[mRNA, extraction]/, response - end - def test_02_query_sparqle_rdf_E_MTAB + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response + end + + def test_02_check_rdf_with_ToxBank_specific_fields_on_E_MTAB id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - #test_all - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/`.chomp - assert_match /[https\:\/\/toxbanktest2, https\:\/\/toxbank\-dev]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + assert_match /[Investigation Identifier, E\-MTAB\-798]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + assert_match /[Investigation Title, Open TG\-GATEs \(in vitro, human\)]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + assert_match /[Investigation Description, The Toxicogenomics Project was a 5\-year collaborative project]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + assert_match /[Owning Organisation URI, TBO\:G176]/, response #test_id_query_sparqle response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - #TODO fix givenname - assert_match /[title, EMBL\-EBI, hasStudy, S2008, hasMember, ISA_60553]/, response + assert_match /[Consortium URI, TBC:G2]/, response #test_resource_ISA - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/ISA_60553`.chomp - assert_match /[givenname, Ruth, family\_name, Akhtar]/, response - #test_metadata_query_sparqle - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/metadata`.chomp - assert_match /[I2]/, response - #test_resource_Investigation - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/I2`.chomp - #TODO assert_match /[title, abstract]/, response - assert_match /[S2008]/, response - #test_resource_Study - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/S2008`.chomp - assert_match /[TG\-GATEs]/, response - assert_match /[hasAssay, A1838, hasProtocol, P_2010]/, response - #test_resource_Assay - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/A1838`.chomp - #TODO fix Assay content - assert_match /Assay/, response - #test_resource_Protocol - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2/P_2010`.chomp - assert_match /[label, P\-MTAB\-23090]/, response - end + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + assert_match /[Investigation keywords, TBK\:Fluxomics]/, response + end + end -- cgit v1.2.3 From fa546277d7bfba28d1461de2bb87a257d30f1504 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 11:27:05 +0200 Subject: required opentox-server --- Gemfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Gemfile b/Gemfile index 8d63ad8..9d9cd0e 100644 --- a/Gemfile +++ b/Gemfile @@ -3,3 +3,4 @@ source 'https://rubygems.org' # Specify your gem's dependencies in opentox-test.gemspec gemspec gem "opentox-client", :path => "~/opentox-client" +gem "opentox-server", :path => "~/opentox-server" -- cgit v1.2.3 From 6d5fd01d04673b6f2bcfa242f71988b3bc1a0b03 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 11:28:40 +0200 Subject: update valid test data/add rdf_check --- test/data/toxbank-investigation/valid/BII-I-1.n3 | 32139 ++++++++++--------- test/data/toxbank-investigation/valid/BII-I-1.rdf | 32139 ++++++++++--------- test/data/toxbank-investigation/valid/BII-I-1.zip | Bin 13225 -> 13684 bytes .../valid/E-MTAB-798_philippe.zip | Bin 111567 -> 111835 bytes test/rdf_check.rb | 16 +- 5 files changed, 34370 insertions(+), 29924 deletions(-) diff --git a/test/data/toxbank-investigation/valid/BII-I-1.n3 b/test/data/toxbank-investigation/valid/BII-I-1.n3 index 6c6fb4a..3ca1c0d 100644 --- a/test/data/toxbank-investigation/valid/BII-I-1.n3 +++ b/test/data/toxbank-investigation/valid/BII-I-1.n3 @@ -1,19648 +1,21871 @@ -@prefix : . +@prefix : . @prefix dc: . @prefix rdfs: . +@prefix tb: . +@prefix foaf: . @prefix isa: . @prefix owl: . @prefix xsd: . @prefix rdf: . @prefix dcterms: . -:MN1290 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.43" ; - isa:hasInputNode :MN735 ; - isa:hasOutputNode :MN396 ; - isa:hasProtocolApplication - :PA2647 ; - isa:hasStudy :S17 . - -:MN2153 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.30" ; - isa:hasInputNode :MN678 ; - isa:hasOutputNode :MN789 ; - isa:hasStudy :S17 . +:DAN405 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.40" ; + isa:hasInputNode :MN2178 ; + isa:hasOutputNode :DN1834 ; + isa:hasStudy :S2 . -:MN795 +:MN1878 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.146:out:0" ; - isa:hasMaterial :M2785 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.29:out:0" ; + isa:hasMaterial :M2234 ; + isa:hasStudy :S2 . -:M2764 +:M2495 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" . - -:DPN1494 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.37" ; - isa:hasInputNode :DN355 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot1" . -:MN1145 +:MN83 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.26" ; - isa:hasInputNode :MN1066 ; - isa:hasOutputNode :MN652 ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.13" ; + isa:hasInputNode :MN1979 ; + isa:hasOutputNode :MN1835 ; isa:hasProtocolApplication - :PA2244 ; - isa:hasStudy :S17 . - -:MN476 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.67:out:0" ; - isa:hasMaterial :M3040 ; - isa:hasStudy :S17 . + :PA2459 ; + isa:hasStudy :S1 . -:DPN1530 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.50" ; - isa:hasInputNode :DN500 ; - isa:hasOutputNode :DN281 ; 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isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:MN330 +:MN1522 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.66:out:0" ; - isa:hasMaterial :M3229 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.38:out:0" ; + isa:hasMaterial :M2556 ; + isa:hasStudy :S2 . -:MN1328 +:PA3692 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . + +:MN585 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.31" ; - isa:hasInputNode :MN1126 ; - isa:hasOutputNode :MN387 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.35" ; + isa:hasInputNode :MN1784 ; + isa:hasOutputNode :MN1885 ; isa:hasProtocolApplication - :PA2716 ; - isa:hasStudy :S17 . + :PA3451 ; + isa:hasStudy :S2 . -:PA2763 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . +:OE3549 + a isa:OntologyEntry . -:DAN1525 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.69" ; - isa:hasInputNode :MN743 ; - isa:hasOutputNode :DN1097 ; - isa:hasStudy :S17 . +:M2730 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3931" . -:MN1215 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.17" ; - isa:hasInputNode :MN334 ; - isa:hasOutputNode :MN689 ; - isa:hasProtocolApplication - :PA2452 ; - isa:hasStudy :S17 . +:M3768 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.1-aliquot8" . -:DPN1928 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.10" ; - isa:hasInputNode :DN341 ; - isa:hasOutputNode :DN812 ; - isa:hasStudy :S17 . +:M2320 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot10" . -:MN1264 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.5" ; - isa:hasInputNode :MN750 ; - isa:hasOutputNode :MN960 ; - isa:hasProtocolApplication - :PA2590 ; - isa:hasStudy :S17 . +:DN1690 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.24:out:0" ; + isa:hasData :D3517 ; + isa:hasStudy :S2 . -:MN1901 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.52" ; - isa:hasInputNode :MN238 ; - isa:hasOutputNode :MN742 ; - isa:hasProtocolApplication - :PA3409 ; - isa:hasStudy :S17 . +:MN1526 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.58:out:0" ; + isa:hasMaterial :M2365 ; + isa:hasStudy :S2 . -:MN1151 +:MN707 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.5" ; - isa:hasInputNode :MN508 ; - isa:hasOutputNode :MN750 ; - isa:hasProtocolApplication - :PA2262 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.28" ; + isa:hasInputNode :MN1881 ; + isa:hasOutputNode :MN1510 ; + isa:hasStudy :S2 . -:PA2768 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . +:DN1978 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.30:out:0" ; + isa:hasData 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:PA2446 ; - isa:hasStudy :S17 . +:MN1670 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.103:out:0" ; + isa:hasMaterial :M2976 ; + isa:hasStudy :S2 . -:MN966 +:OE3616 + a isa:OntologyEntry . + +:D3163 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC63_Carbon_0.20_External_3_1.txt" ; + dcterms:title "JIC63_Carbon_0.20_External_3_1.txt" . + +:MN1898 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.9:out:0" ; - isa:hasMaterial :M2547 ; - isa:hasStudy :S16 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.12:out:0" ; + isa:hasMaterial :M3395 ; + isa:hasStudy :S2 . -:DPN1528 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.52" ; - isa:hasInputNode :DN385 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:DN1753 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.14:out:0" ; + isa:hasData :D3542 ; + isa:hasStudy :S2 . -:M2734 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.07-aliquot5" . +:PA2809 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:DPN1468 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.27" ; - isa:hasInputNode :DN680 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1110 + a isa:Protocol ; + rdfs:label "EukGE-WS4"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\EukGE-WS4" ; + dcterms:description "For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip �_� Expression Analysis technical manual. GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5mins, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 �_�l 1x hybridisation buffer and incubated at 45 C for 10 min. 200 �_�l of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1923 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.11" ; - isa:hasInputNode :DN802 ; - isa:hasOutputNode :DN728 ; - isa:hasStudy :S17 . +:D2707 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_derived_data:a_proteome.datatransformation1" ; + isa:hasFactorValue :FV2710 , :FV2709 ; + dcterms:title "datatransformation1" . -:DAN1462 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.78" ; - isa:hasInputNode :MN453 ; - isa:hasOutputNode :DN778 ; - isa:hasStudy :S17 . +:M2681 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3953" . -:D2923 +:D2637 a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC22_Phosphate_0.10_Internal_1_1.txt" . + isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3911" ; + dcterms:title "SCAN:MEXP:3911" . -:MN2216 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.17" ; - isa:hasInputNode :MN756 ; - isa:hasOutputNode :MN1047 ; - isa:hasStudy :S17 . +:MN1959 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16:out:0" ; + isa:hasMaterial :M2452 ; + isa:hasStudy :S2 . -:MN1214 +:MN10 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16" ; - isa:hasInputNode :MN559 ; - isa:hasOutputNode :MN861 ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25" ; + isa:hasInputNode :MN2210 ; + isa:hasOutputNode :MN2103 ; isa:hasProtocolApplication - :PA2449 ; - isa:hasStudy :S17 . - -:MN1856 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.21" ; - isa:hasInputNode :MN762 ; - isa:hasOutputNode :MN834 ; - isa:hasStudy :S17 . + :PA2241 ; + isa:hasStudy :S2 . -:PA3385 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:PA3489 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1112 . -:MN1900 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.41" ; - isa:hasInputNode :MN242 ; - isa:hasOutputNode :MN944 ; - isa:hasStudy :S17 . +:PA2670 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:MN967 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.94:out:0" ; - isa:hasMaterial :M2515 ; - isa:hasStudy :S17 . +:DPN847 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.7" ; + isa:hasInputNode :DN1358 ; + isa:hasOutputNode :DN1585 ; + isa:hasStudy :S2 . -:MN1152 +:MN587 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.0" ; - isa:hasInputNode :MN372 ; - isa:hasOutputNode :MN540 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.37" ; + isa:hasInputNode :MN1927 ; + isa:hasOutputNode :MN1668 ; isa:hasProtocolApplication - :PA2265 ; - isa:hasStudy :S17 . + :PA3455 ; + isa:hasStudy :S2 . -:MN1212 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.14" ; - isa:hasInputNode :MN587 ; - isa:hasOutputNode :MN897 ; - isa:hasProtocolApplication - :PA2443 ; - isa:hasStudy :S17 . +:DAN323 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.81" ; + isa:hasInputNode :MN2034 ; + isa:hasOutputNode :DN1455 ; + isa:hasStudy :S2 . -:MN400 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.91:out:0" ; - isa:hasMaterial :M2765 ; - isa:hasStudy :S17 . +:FV3737 + a isa:FactorValue . -:MN788 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.26:out:0" ; - isa:hasMaterial :M3124 ; - isa:hasStudy :S17 . +:A1310 + a isa:Assay . -:MN2214 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.15" ; - isa:hasInputNode :MN232 ; - isa:hasOutputNode :MN362 ; - isa:hasStudy :S17 . +:P_1111 + a isa:Protocol ; + rdfs:label "growth protocol"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\growth protocol" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:M2479 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot4" . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:M3408 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.07-aliquot5" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorously or 15 s, then 5min incubation at room temperature. -:M2733 +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. + +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl buffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. + +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. + + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . + +:FV3732 + a isa:FactorValue . + +:PA2725 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1103 . + +:M2732 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:G-0.07-aliquot5" . + isa:hasAccessionID "BII-S-1:sample:C-0.07-aliquot6" . -:M2801 +:M2326 a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3922" . + isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot8" . -:PA2226 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . +:DN2062 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.20:out:0" ; + isa:hasData :D3026 ; + isa:hasStudy :S2 . -:DPN1529 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.51" ; - isa:hasInputNode :DN1042 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:OE3546 + a isa:OntologyEntry . -:MN2215 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.16" ; - isa:hasInputNode :MN771 ; - isa:hasOutputNode :MN489 ; - isa:hasStudy :S17 . +:PA2343 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:D3430 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3917" . +:OE3614 + a isa:OntologyEntry . -:MN1211 +:MN588 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.13" ; - isa:hasInputNode :MN455 ; - isa:hasOutputNode :MN553 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.36" ; + isa:hasInputNode :MN1904 ; + isa:hasOutputNode :MN2003 ; isa:hasProtocolApplication - :PA2440 ; - isa:hasStudy :S17 . + :PA3457 ; + isa:hasStudy :S2 . -:MN968 +:MN1672 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.46:out:0" ; - isa:hasMaterial :M2636 ; - isa:hasStudy :S17 . - -:MN1262 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.8" ; - isa:hasInputNode :MN456 ; - isa:hasOutputNode :MN554 ; - isa:hasProtocolApplication - :PA2586 ; - isa:hasStudy :S17 . - -:M2736 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . - -:PA3382 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.74:out:0" ; + isa:hasMaterial :M3482 ; + isa:hasStudy :S2 . -:DPN1466 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.26" ; - isa:hasInputNode :DN222 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1112 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:DPN1812 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.13" ; - isa:hasInputNode :DN713 ; - isa:hasOutputNode :DN600 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:MN765 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.10:out:0" ; - isa:hasMaterial :M2433 ; - isa:hasStudy :S17 . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5min incubation at room temperature. -:DPN1526 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.53" ; - isa:hasInputNode :DN495 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN2218 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.19" ; - isa:hasInputNode :MN252 ; - isa:hasOutputNode :MN255 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:DPN1925 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.12" ; - isa:hasInputNode :DN891 ; - isa:hasOutputNode :DN534 ; - isa:hasStudy :S17 . +7. After precipitation (20 C for 1 h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:DAN1460 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.79" ; - isa:hasInputNode :MN677 ; - isa:hasOutputNode :DN766 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). 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+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.68" ; + isa:hasInputNode :MN1471 ; + isa:hasOutputNode :DN2146 ; + isa:hasStudy :S2 . -:PA3579 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:M2813 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" . -:M2699 +:OE3043 + a isa:OntologyEntry . + +:M3833 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot6" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot9" . -:MN559 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.16:out:0" ; - isa:hasMaterial :M2450 ; - isa:hasStudy :S17 . +:I1115 + a isa:Investigation ; + isa:hasAccessionID "BII-I-1" ; + isa:hasOwner :ISA_3977 , :ISA_3976 , :ISA_3975 ; + isa:hasStudy :S1 , :S2 ; + dcterms:abstract """Background +Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. +Results +Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. +Conclusion +This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ; + dcterms:created "29 Apr 2007 20:00:00 GMT" ; + dcterms:issued "9 Mar 2009 21:00:00 GMT" ; + dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" . + +:OE3000 + a isa:OntologyEntry . -:PA3465 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:ProtocolApplication + rdfs:subClassOf isa:Accessible . -:PA3578 +:MN786 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . - -:D2599 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3910" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.49" ; + isa:hasInputNode :MN2174 ; + isa:hasOutputNode :MN2151 ; + isa:hasStudy :S2 . -:D3435 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3918" . +:DPN523 + a isa:DataProcessing ; 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Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. Gene expression at the mRNA level was investigated by transcriptome analysis using Affymetrix hybridization arrays." ; + dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" . -:MN302 +:MN1355 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.40:out:0" ; - isa:hasMaterial :M2331 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.8:out:0" ; + isa:hasMaterial :M2935 ; + isa:hasStudy :S1 . -:M2376 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.2-aliquot6" . +:A1236 + a isa:Assay . -:DPN1625 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.85" ; - isa:hasInputNode :DN482 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:MN2103 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25:out:0" ; + isa:hasMaterial :M2243 ; + isa:hasStudy :S2 . -:M2575 - a isa:Material ; 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- isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.3" ; - isa:hasInputNode :DN807 ; - isa:hasOutputNode :DN916 ; - isa:hasStudy :S16 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.91" ; + isa:hasInputNode :DN1472 ; + isa:hasOutputNode :DN1379 ; + isa:hasStudy :S2 . -:MN506 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.33:out:0" ; - isa:hasMaterial :M2332 ; - isa:hasStudy :S17 . +:A1191 + a isa:Assay . -:D2969 - a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC38_Ethanol_0.07_Internal_2_1.txt" . +:OE3166 + a isa:OntologyEntry . -:MN1005 +:OE3371 + a isa:OntologyEntry . + +:MN1844 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25:out:0" ; - isa:hasMaterial :M2243 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.15:out:0" ; + isa:hasMaterial :M3263 ; + isa:hasStudy :S2 . -:M3452 +:M2783 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.07-aliquot5" . -:M3077 +:M2578 a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC72_Nitrogen_0.20_External_3_1" . + isa:hasAccessionID "BII-S-1:sample:S-0.07-aliquot7" . -:M2363 +:M3507 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC82_Sulphate_0.07_External_1_3" . -:MN216 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.2.4.3:out:0" ; - isa:hasMaterial :M2402 ; - isa:hasStudy :S16 . +:M3714 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.07-aliquot6" . -:DN258 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.75:out:0" ; - isa:hasData :D3036 ; - isa:hasStudy :S17 . +:DPN404 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.8" ; + isa:hasInputNode :DN1669 ; + isa:hasOutputNode :DN1379 ; + isa:hasStudy :S2 . -:MN1891 +:MN296 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.48" ; - isa:hasInputNode :MN238 ; - isa:hasOutputNode :MN717 ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.9" ; + isa:hasInputNode :MN1790 , :MN1836 , :MN1581 ; + isa:hasOutputNode :MN1640 ; isa:hasProtocolApplication - :PA3398 ; - isa:hasStudy :S17 . + :PA2950 ; + isa:hasStudy :S2 . -:PA2262 +:MN694 a isa:MaterialProcessing ; - isa:hasProtocol :P_1131 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.10" ; + isa:hasInputNode :MN2183 ; + isa:hasOutputNode :MN2114 ; + isa:hasStudy :S2 . -:DAN1843 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.6.7.1" ; - isa:hasInputNode :MN591 ; - isa:hasOutputNode :DN997 ; - isa:hasStudy :S16 . +:DN1797 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.26:out:0" ; + isa:hasData :D3694 ; + isa:hasStudy :S2 . -:DPN1638 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.6" ; - isa:hasInputNode :DN723 ; - isa:hasOutputNode :DN786 ; - isa:hasStudy :S16 . +:MN1058 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.22" ; + isa:hasInputNode :MN1350 ; + isa:hasOutputNode :MN1353 ; + isa:hasStudy :S2 . -:M3517 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.07-aliquot2" . +:DN1716 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.26:out:0" ; + isa:hasData :D3521 ; + isa:hasStudy :S2 . -:D3039 - a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC46_GlucoseO2_0.07_Internal_1_3.txt" . +:OE2987 + a isa:OntologyEntry . -:MN2140 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.65" ; - isa:hasInputNode :MN474 ; - isa:hasOutputNode :MN610 ; - isa:hasProtocolApplication - :PA3547 ; - isa:hasStudy :S17 . +:A1251 + a isa:Assay . -:MN858 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.2:out:0" ; - isa:hasMaterial :M2780 ; - isa:hasStudy :S17 . +:P_1103 + a isa:Protocol ; + rdfs:label "EukGE-WS4"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\EukGE-WS4" ; + dcterms:description "For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip �_� Expression Analysis technical manual. GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5 min, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 ul 1x hybridisation buffer and incubated at 45 C for 10 min. 200 ul of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16 hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1783 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.41" ; - isa:hasInputNode :DN378 ; - isa:hasOutputNode :DN413 ; - isa:hasStudy :S17 . +:M3446 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:P-0.1-aliquot3" . -:M3326 +:M2579 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot7" . -:MN1728 +:PA2518 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . + +:M3506 + a isa:Material ; + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC85_Sulphate_0.10_External_1_1" . + +:PA3917 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . + +:FV3673 + a isa:FactorValue . + +:PA3872 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . + +:MN295 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.26" ; - isa:hasInputNode :MN330 ; - isa:hasOutputNode :MN851 ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.7" ; + isa:hasInputNode :MN1581 ; + isa:hasOutputNode :MN1765 ; isa:hasProtocolApplication - :PA3228 ; - isa:hasStudy :S17 . + :PA2949 ; + isa:hasStudy :S2 . -:MN215 +:MN1841 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.17:out:0" ; - isa:hasMaterial :M3095 ; - isa:hasStudy :S17 . - -:M2364 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.69:out:0" ; + isa:hasMaterial :M3188 ; + isa:hasStudy :S2 . -:MN1890 +:MN693 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.36" ; - isa:hasInputNode :MN931 ; - isa:hasOutputNode :MN793 ; - isa:hasStudy :S17 . - -:M2942 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC50_GlucoseO2_0.10_Internal_2_1" . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.29" ; + isa:hasInputNode :MN1360 ; + isa:hasOutputNode :MN1686 ; + isa:hasProtocolApplication + :PA3657 ; + isa:hasStudy :S2 . -:M3184 - a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot3" . +:A1250 + a isa:Assay . -:DN481 +:DN1501 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.18:out:0" ; - isa:hasData :D2938 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_proteome.7.8.1:out:0" ; + isa:hasData :D2707 ; + isa:hasStudy :S2 . -:PA3415 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:MN1642 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.10:out:0" ; + isa:hasMaterial :M2431 ; + isa:hasStudy :S1 . -:DPN1637 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.7" ; - isa:hasInputNode :DN464 ; - isa:hasOutputNode :DN914 ; - isa:hasStudy :S16 . +:P_1102 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:MN280 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.110:out:0" ; - isa:hasMaterial :M2835 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5 min. -:M2587 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3916" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5 min incubation at room temperature. -:DN537 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.18:out:0" ; - isa:hasData :D3291 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN1729 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.25" ; - isa:hasInputNode :MN610 ; - isa:hasOutputNode :MN383 ; - isa:hasProtocolApplication - :PA3230 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:D3338 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3924" . +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:MN370 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.2:out:0" ; - isa:hasMaterial :M2607 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:M2361 +:MN1057 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.5" ; + isa:hasInputNode :MN1375 ; + isa:hasOutputNode :MN1402 ; + isa:hasStudy :S2 . + +:M2628 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.07-aliquot6" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot6" . -:MN218 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.37:out:0" ; - isa:hasMaterial :M2570 ; - isa:hasStudy :S17 . +:DN1918 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.35:out:0" ; + isa:hasData :D3384 ; + isa:hasStudy :S2 . -:M3001 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC9_Carbon_0.20_Internal_3_1" . +:OE3164 + a isa:OntologyEntry . -:M2771 +:M3712 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.2-aliquot5" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.07-aliquot7" . -:PA3418 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:hasProtocolApplication + a owl:ObjectProperty ; + rdfs:domain isa:Processing ; + rdfs:range isa:ProtocolApplication . -:DPN1636 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.8" ; - isa:hasInputNode :DN297 ; - isa:hasOutputNode :DN744 ; - isa:hasStudy :S16 . +:FV3672 + a isa:FactorValue . -:M3515 +:M3505 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.2-aliquot4" . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC86_Sulphate_0.10_External_2_1" . -:MN371 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:s_BII-S-2.0.2.0:in:0" ; - isa:hasMaterial :M2355 ; - isa:hasStudy :S16 . +:M2785 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . -:M3186 +:OE3586 + a isa:OntologyEntry . + +:FV3662 + a isa:FactorValue . + +:M2775 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot4" . + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3942" . + +:DN1709 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.30:out:0" ; + isa:hasData :D3725 ; + isa:hasStudy :S2 . -:MN217 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.38:out:0" ; - isa:hasMaterial :M2707 ; - isa:hasStudy :S17 . +:D3119 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC16_Nitrogen_0.20_Internal_1_1.txt" ; + dcterms:title "JIC16_Nitrogen_0.20_Internal_1_1.txt" . -:MN282 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_proteome.4.5.2:out:0" ; - isa:hasMaterial :M2759 ; - isa:hasStudy :S17 . +:FV2968 + a isa:FactorValue . -:M2418 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_proteome.N-0.2" . +:OE2990 + a isa:OntologyEntry . -:DPN1635 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.90" ; - isa:hasInputNode :DN886 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:FV3708 + a isa:FactorValue . -:MN449 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.7:out:0" ; 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GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5mins, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 �_�l 1x hybridisation buffer and incubated at 45 C for 10 min. 200 �_�l of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1923 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.11" ; - isa:hasInputNode :DN802 ; - isa:hasOutputNode :DN728 ; - isa:hasStudy :S17 . +:D2707 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_derived_data:a_proteome.datatransformation1" ; + isa:hasFactorValue :FV2710 , :FV2709 ; + dcterms:title "datatransformation1" . -:DAN1462 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.78" ; - isa:hasInputNode :MN453 ; - isa:hasOutputNode :DN778 ; - isa:hasStudy :S17 . +:M2681 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3953" . -:D2923 +:D2637 a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC22_Phosphate_0.10_Internal_1_1.txt" . + isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3911" ; + dcterms:title "SCAN:MEXP:3911" . -:MN2216 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.17" ; - isa:hasInputNode :MN756 ; - isa:hasOutputNode :MN1047 ; - isa:hasStudy :S17 . +:MN1959 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16:out:0" ; + isa:hasMaterial :M2452 ; + isa:hasStudy :S2 . -:MN1214 +:MN10 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16" ; - isa:hasInputNode :MN559 ; - isa:hasOutputNode :MN861 ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25" ; + isa:hasInputNode :MN2210 ; + isa:hasOutputNode :MN2103 ; isa:hasProtocolApplication - :PA2449 ; - isa:hasStudy :S17 . - -:MN1856 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.21" ; - isa:hasInputNode :MN762 ; - isa:hasOutputNode :MN834 ; - isa:hasStudy :S17 . + :PA2241 ; + isa:hasStudy :S2 . -:PA3385 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:PA3489 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1112 . -:MN1900 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.41" ; - isa:hasInputNode :MN242 ; - isa:hasOutputNode :MN944 ; - isa:hasStudy :S17 . +:PA2670 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:MN967 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.94:out:0" ; - isa:hasMaterial :M2515 ; - isa:hasStudy :S17 . +:DPN847 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.7" ; + isa:hasInputNode :DN1358 ; + isa:hasOutputNode :DN1585 ; + isa:hasStudy :S2 . -:MN1152 +:MN587 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.0" ; - isa:hasInputNode :MN372 ; - isa:hasOutputNode :MN540 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.37" ; + isa:hasInputNode :MN1927 ; + isa:hasOutputNode :MN1668 ; isa:hasProtocolApplication - :PA2265 ; - isa:hasStudy :S17 . + :PA3455 ; + isa:hasStudy :S2 . -:MN1212 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.14" ; - isa:hasInputNode :MN587 ; - isa:hasOutputNode :MN897 ; - isa:hasProtocolApplication - :PA2443 ; - isa:hasStudy :S17 . +:DAN323 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.81" ; + isa:hasInputNode :MN2034 ; + isa:hasOutputNode :DN1455 ; + isa:hasStudy :S2 . -:MN400 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.91:out:0" ; - isa:hasMaterial :M2765 ; - isa:hasStudy :S17 . +:FV3737 + a isa:FactorValue . -:MN788 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.26:out:0" ; - isa:hasMaterial :M3124 ; - isa:hasStudy :S17 . +:A1310 + a isa:Assay . -:MN2214 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.15" ; - isa:hasInputNode :MN232 ; - isa:hasOutputNode :MN362 ; - isa:hasStudy :S17 . +:P_1111 + a isa:Protocol ; + rdfs:label "growth protocol"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\growth protocol" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:M2479 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot4" . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:M3408 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.07-aliquot5" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorously or 15 s, then 5min incubation at room temperature. -:M2733 +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. + +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl buffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. + +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. + + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . + +:FV3732 + a isa:FactorValue . + +:PA2725 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1103 . + +:M2732 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:G-0.07-aliquot5" . + isa:hasAccessionID "BII-S-1:sample:C-0.07-aliquot6" . -:M2801 +:M2326 a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3922" . + isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot8" . -:PA2226 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . +:DN2062 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.20:out:0" ; + isa:hasData :D3026 ; + isa:hasStudy :S2 . -:DPN1529 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.51" ; - isa:hasInputNode :DN1042 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:OE3546 + a isa:OntologyEntry . -:MN2215 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.16" ; - isa:hasInputNode :MN771 ; - isa:hasOutputNode :MN489 ; - isa:hasStudy :S17 . +:PA2343 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:D3430 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3917" . +:OE3614 + a isa:OntologyEntry . -:MN1211 +:MN588 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.13" ; - isa:hasInputNode :MN455 ; - isa:hasOutputNode :MN553 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.36" ; + isa:hasInputNode :MN1904 ; + isa:hasOutputNode :MN2003 ; isa:hasProtocolApplication - :PA2440 ; - isa:hasStudy :S17 . + :PA3457 ; + isa:hasStudy :S2 . -:MN968 +:MN1672 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.46:out:0" ; - isa:hasMaterial :M2636 ; - isa:hasStudy :S17 . - -:MN1262 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.8" ; - isa:hasInputNode :MN456 ; - isa:hasOutputNode :MN554 ; - isa:hasProtocolApplication - :PA2586 ; - isa:hasStudy :S17 . - -:M2736 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . - -:PA3382 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.74:out:0" ; + isa:hasMaterial :M3482 ; + isa:hasStudy :S2 . -:DPN1466 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.26" ; - isa:hasInputNode :DN222 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1112 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:DPN1812 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.13" ; - isa:hasInputNode :DN713 ; - isa:hasOutputNode :DN600 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:MN765 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.10:out:0" ; - isa:hasMaterial :M2433 ; - isa:hasStudy :S17 . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5min incubation at room temperature. -:DPN1526 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.53" ; - isa:hasInputNode :DN495 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN2218 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.19" ; - isa:hasInputNode :MN252 ; - isa:hasOutputNode :MN255 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:DPN1925 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.12" ; - isa:hasInputNode :DN891 ; - isa:hasOutputNode :DN534 ; - isa:hasStudy :S17 . +7. After precipitation (20 C for 1 h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:DAN1460 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.79" ; - isa:hasInputNode :MN677 ; - isa:hasOutputNode :DN766 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:DN571 +:DN1544 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.8:out:0" ; - isa:hasData :D3058 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.10:out:0" ; + isa:hasData :D3348 ; + isa:hasStudy :S1 . -:MN480 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.75:out:0" ; - isa:hasMaterial :M3237 ; - isa:hasStudy :S17 . +:D2639 + a isa:Data ; + isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3911" ; + isa:hasFactorValue :FV2642 , :FV2641 ; + dcterms:title "SCAN:MEXP:3911" . -:M3406 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.2-aliquot10" . +:OE3271 + a isa:OntologyEntry . -:MN1210 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.12" ; - isa:hasInputNode :MN317 ; - isa:hasOutputNode :MN549 ; - isa:hasProtocolApplication - :PA2437 ; - isa:hasStudy :S17 . +:D3160 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC69_Nitrogen_0.10_External_3_1.txt" ; + dcterms:title "JIC69_Nitrogen_0.10_External_3_1.txt" . -:MN1854 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.26" ; - isa:hasInputNode :MN753 ; - isa:hasOutputNode :MN788 ; - isa:hasStudy :S17 . +:ISA_1113 + a foaf:Person , isa:Contact ; + foaf:family_name "Leo"^^xsd:string ; + foaf:givenname "Zeef"^^xsd:string . + +:MN1895 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.59:out:0" ; + isa:hasMaterial :M3822 ; + isa:hasStudy :S2 . -:MN764 +:MN1671 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.36:out:0" ; - isa:hasMaterial :M2317 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.66:out:0" ; + isa:hasMaterial :M2733 ; + isa:hasStudy :S2 . -:MN1150 +:MN589 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.21" ; - isa:hasInputNode :MN1108 ; - isa:hasOutputNode :MN976 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.38" ; + isa:hasInputNode :MN2192 ; + isa:hasOutputNode :MN1364 ; isa:hasProtocolApplication - :PA2259 ; - isa:hasStudy :S17 . + :PA3459 ; + isa:hasStudy :S2 . -:MN2217 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.18" ; - isa:hasInputNode :MN276 ; - isa:hasOutputNode :MN637 ; - isa:hasStudy :S17 . +:DN1756 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.0:out:0" ; + isa:hasData :D2593 ; + isa:hasStudy :S2 . + +:DPN849 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.6" ; + isa:hasInputNode :DN1358 ; + isa:hasOutputNode :DN1585 ; + isa:hasStudy :S2 . + +:DN1543 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.41:out:0" ; + isa:hasData :D3144 ; + isa:hasStudy :S2 . -:M2880 +:PA2767 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . + +:M2324 a isa:Material ; - isa:hasAccessionID "BII-S-2:extract:a_microarray.NZ_0hrs_Sample_2_Extract" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.07-aliquot10" . -:PA2553 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1131 . +:MN1804 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.4:out:0" ; + isa:hasMaterial :M2248 ; + isa:hasStudy :S2 . -:DAN1745 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.2" ; - isa:hasInputNode :MN234 ; - isa:hasOutputNode :DN718 ; - isa:hasStudy :S17 . +:FV3295 + a isa:FactorValue . -:MN1771 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.2.4.8" ; - isa:hasInputNode :MN257 ; - isa:hasOutputNode :MN1046 ; - isa:hasProtocolApplication - :PA3286 ; - isa:hasStudy :S16 . +:M3619 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.2-aliquot10" . -:M2319 +:M2520 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot10" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.P-0.2-aliquot9" . -:DN937 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.101:out:0" ; - isa:hasData :D3460 ; - isa:hasStudy :S17 . +:PA2723 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1103 . -:MN2210 +:MN850 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.83" ; - isa:hasInputNode :MN411 ; - isa:hasOutputNode :MN401 ; + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.129" ; + isa:hasInputNode :MN1335 ; + isa:hasOutputNode :MN1436 ; isa:hasProtocolApplication - :PA3582 ; - isa:hasStudy :S17 . - -:PA3163 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1138 . + :PA3875 ; + isa:hasStudy :S2 . -:MN336 +:MN1894 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.2.4.7:out:0" ; - isa:hasMaterial :M2538 ; - isa:hasStudy :S16 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.99:out:0" ; + isa:hasMaterial :M3462 ; + isa:hasStudy :S2 . -:DN704 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.20:out:0" ; - isa:hasData :D3340 ; - isa:hasStudy :S17 . +:MN1388 + a isa:MaterialNode ; 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+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.68" ; + isa:hasInputNode :MN1471 ; + isa:hasOutputNode :DN2146 ; + isa:hasStudy :S2 . -:PA3579 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:M2813 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" . -:M2699 +:OE3043 + a isa:OntologyEntry . + +:M3833 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot6" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot9" . -:MN559 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.16:out:0" ; - isa:hasMaterial :M2450 ; - isa:hasStudy :S17 . +:I1115 + a isa:Investigation ; + isa:hasAccessionID "BII-I-1" ; + isa:hasOwner :ISA_3977 , :ISA_3976 , :ISA_3975 ; + isa:hasStudy :S1 , :S2 ; + dcterms:abstract """Background +Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. +Results +Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. +Conclusion +This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ; + dcterms:created "29 Apr 2007 20:00:00 GMT" ; + dcterms:issued "9 Mar 2009 21:00:00 GMT" ; + dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" . + +:OE3000 + a isa:OntologyEntry . -:PA3465 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:ProtocolApplication + rdfs:subClassOf isa:Accessible . -:PA3578 +:MN786 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . - -:D2599 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3910" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.49" ; + isa:hasInputNode :MN2174 ; + isa:hasOutputNode :MN2151 ; + isa:hasStudy :S2 . -:D3435 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3918" . +:DPN523 + a isa:DataProcessing ; 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Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. 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GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5 min, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 ul 1x hybridisation buffer and incubated at 45 C for 10 min. 200 ul of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16 hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1783 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.41" ; - isa:hasInputNode :DN378 ; - isa:hasOutputNode :DN413 ; - isa:hasStudy :S17 . +:M3446 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:P-0.1-aliquot3" . -:M3326 +:M2579 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot7" . -:MN1728 +:PA2518 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . + +:M3506 + a isa:Material ; + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC85_Sulphate_0.10_External_1_1" . + +:PA3917 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . + +:FV3673 + a isa:FactorValue . + +:PA3872 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . + +:MN295 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.26" ; - isa:hasInputNode :MN330 ; - isa:hasOutputNode :MN851 ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.7" ; + isa:hasInputNode :MN1581 ; + isa:hasOutputNode :MN1765 ; isa:hasProtocolApplication - :PA3228 ; - isa:hasStudy :S17 . + :PA2949 ; + isa:hasStudy :S2 . -:MN215 +:MN1841 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.17:out:0" ; - isa:hasMaterial :M3095 ; - isa:hasStudy :S17 . - -:M2364 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.69:out:0" ; + isa:hasMaterial :M3188 ; + isa:hasStudy :S2 . -:MN1890 +:MN693 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.36" ; - isa:hasInputNode :MN931 ; - isa:hasOutputNode :MN793 ; - isa:hasStudy :S17 . - -:M2942 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC50_GlucoseO2_0.10_Internal_2_1" . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.29" ; + isa:hasInputNode :MN1360 ; + isa:hasOutputNode :MN1686 ; + isa:hasProtocolApplication + :PA3657 ; + isa:hasStudy :S2 . -:M3184 - a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot3" . +:A1250 + a isa:Assay . -:DN481 +:DN1501 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.18:out:0" ; - isa:hasData :D2938 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_proteome.7.8.1:out:0" ; + isa:hasData :D2707 ; + isa:hasStudy :S2 . -:PA3415 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:MN1642 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.10:out:0" ; + isa:hasMaterial :M2431 ; + isa:hasStudy :S1 . -:DPN1637 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.7" ; - isa:hasInputNode :DN464 ; - isa:hasOutputNode :DN914 ; - isa:hasStudy :S16 . +:P_1102 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:MN280 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.110:out:0" ; - isa:hasMaterial :M2835 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5 min. -:M2587 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3916" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5 min incubation at room temperature. -:DN537 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.18:out:0" ; - isa:hasData :D3291 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN1729 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.25" ; - isa:hasInputNode :MN610 ; - isa:hasOutputNode :MN383 ; - isa:hasProtocolApplication - :PA3230 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:D3338 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3924" . +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:MN370 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.2:out:0" ; - isa:hasMaterial :M2607 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:M2361 +:MN1057 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.5" ; + isa:hasInputNode :MN1375 ; + isa:hasOutputNode :MN1402 ; + isa:hasStudy :S2 . + +:M2628 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.07-aliquot6" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot6" . -:MN218 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.37:out:0" ; - isa:hasMaterial :M2570 ; - isa:hasStudy :S17 . +:DN1918 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.35:out:0" ; + isa:hasData :D3384 ; + isa:hasStudy :S2 . -:M3001 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC9_Carbon_0.20_Internal_3_1" . +:OE3164 + a isa:OntologyEntry . -:M2771 +:M3712 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.2-aliquot5" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.07-aliquot7" . -:PA3418 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:hasProtocolApplication + a owl:ObjectProperty ; + rdfs:domain isa:Processing ; + rdfs:range isa:ProtocolApplication . -:DPN1636 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.8" ; - isa:hasInputNode :DN297 ; - isa:hasOutputNode :DN744 ; - isa:hasStudy :S16 . +:FV3672 + a isa:FactorValue . -:M3515 +:M3505 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.2-aliquot4" . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC86_Sulphate_0.10_External_2_1" . -:MN371 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:s_BII-S-2.0.2.0:in:0" ; - isa:hasMaterial :M2355 ; - isa:hasStudy :S16 . +:M2785 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . -:M3186 +:OE3586 + a isa:OntologyEntry . + +:FV3662 + a isa:FactorValue . + +:M2775 a 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isa:hasInputNode :DN886 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:FV3708 + a isa:FactorValue . -:MN449 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.7:out:0" ; - isa:hasMaterial :M2285 ; - isa:hasStudy :S17 . +:A1196 + a isa:Assay . -:PA3417 +:MN1004 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.62" ; + isa:hasInputNode :MN1357 ; + isa:hasOutputNode :MN1974 ; + isa:hasProtocolApplication + :PA3934 ; + isa:hasStudy :S2 . -:DN535 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.4:out:0" ; - isa:hasData :D2608 ; - isa:hasStudy :S17 . +:PA2402 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1110 . -:PA3341 +:MN964 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . - -:MN859 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.7:out:0" ; - isa:hasMaterial :M2381 ; - isa:hasStudy :S17 . + isa:hasAccessionID 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isa:hasMaterial :M3061 ; + isa:hasStudy :S2 . -:PA2867 +:D3834 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC91_Ethanol_0.07_External_1_1.txt" ; + dcterms:title "JIC91_Ethanol_0.07_External_1_1.txt" . + +:MN59 a isa:MaterialProcessing ; - isa:hasProtocol :P_1128 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.0" ; + isa:hasInputNode :MN1988 ; + isa:hasOutputNode :MN1583 ; + isa:hasProtocolApplication + :PA2387 ; + isa:hasStudy :S1 . -:DPN1572 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.68" ; - isa:hasInputNode :DN1048 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:MN1346 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.22:out:0" ; + isa:hasMaterial :M2472 ; + isa:hasStudy :S2 . -:M2628 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.1-aliquot6" . +:A1195 + a isa:Assay . -:M2439 - a isa:Material ; - isa:hasAccessionID 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isa:hasOutputNode :MN231 ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.7" ; + isa:hasInputNode :MN1704 ; + isa:hasOutputNode :MN1637 ; isa:hasProtocolApplication - :PA3404 ; - isa:hasStudy :S17 . + :PA2936 ; + isa:hasStudy :S1 . -:MN1724 +:MN965 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.39" ; - isa:hasInputNode :MN796 ; - isa:hasOutputNode :MN1079 ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.62" ; + isa:hasInputNode :MN2112 ; + isa:hasOutputNode :MN1365 ; + isa:hasStudy :S2 . + +:OE3582 + a isa:OntologyEntry . + +:M3891 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.1-aliquot4" . + +:MN58 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.55" ; + isa:hasInputNode :MN1977 ; + isa:hasOutputNode :MN1786 ; isa:hasProtocolApplication - :PA3220 ; - isa:hasStudy :S17 . + :PA2384 ; + isa:hasStudy :S2 . -:M2773 +:M2777 a isa:Material ; - isa:hasAccessionID 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isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.29" ; - isa:hasInputNode :MN404 ; - isa:hasOutputNode :MN864 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.25" ; + isa:hasInputNode :MN1540 ; + isa:hasOutputNode :MN1366 ; isa:hasProtocolApplication - :PA2475 ; - isa:hasStudy :S17 . + :PA2727 ; + isa:hasStudy :S2 . -:M3449 +:M2364 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot8" . + isa:hasAccessionID "BII-S-1:sample:C-0.1-aliquot9" . -:MN860 +:MN1349 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.71:out:0" ; - isa:hasMaterial :M2497 ; - isa:hasStudy :S17 . - -:DPN1976 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.9" ; - isa:hasInputNode :DN260 ; - isa:hasOutputNode :DN487 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.13:out:0" ; + isa:hasMaterial :M2466 ; + isa:hasStudy :S1 . -:MN712 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.89:out:0" ; - isa:hasMaterial :M3521 ; - isa:hasStudy :S17 . +:PA2405 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . -:MN1090 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.41:out:0" ; - isa:hasMaterial :M2322 ; - isa:hasStudy :S17 . +:M3894 + a isa:Material ; + isa:hasAccessionID "BII-S-1:source:culture16" . +: owl:sameAs :I1115 . diff --git a/test/data/toxbank-investigation/valid/BII-I-1.zip b/test/data/toxbank-investigation/valid/BII-I-1.zip index fa56e5a..fbe4cdf 100644 Binary files a/test/data/toxbank-investigation/valid/BII-I-1.zip and b/test/data/toxbank-investigation/valid/BII-I-1.zip differ diff --git a/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip b/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip index c1aa89c..d0d0ffe 100644 Binary files a/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip and b/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip differ diff --git a/test/rdf_check.rb b/test/rdf_check.rb index 587e342..d8838a5 100644 --- a/test/rdf_check.rb +++ b/test/rdf_check.rb @@ -11,17 +11,19 @@ class UploadTest < Test::Unit::TestCase def test_01_check_rdf_with_ToxBank_specific_fields_on_BII_I_1 id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation Identifier, BII\-I\-1]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Owning Organisation URI, TBO\:G176]/, response - #test_id_query_sparqle + assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + assert_match /[Consortium URI, TBC\:G2, Douglas Connect]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Consortium URI, TBC:G2]/, response - #test_resource_ISA + assert_match /[Principal Investigator URI, TBU\:U115, Glenn Myatt]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response end @@ -35,11 +37,9 @@ class UploadTest < Test::Unit::TestCase response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Investigation Description, The Toxicogenomics Project was a 5\-year collaborative project]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Owning Organisation URI, TBO\:G176]/, response - #test_id_query_sparqle + assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Consortium URI, TBC:G2]/, response - #test_resource_ISA + assert_match /[Consortium URI, TBC:G2, Douglas Connect]/, response response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Investigation keywords, TBK\:Fluxomics]/, response end -- cgit v1.2.3 From 34441f556a37a2d55b9ae7bd0486ac594e834c26 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 11:28:40 +0200 Subject: update valid test data/add rdf_check --- test/data/toxbank-investigation/valid/BII-I-1.n3 | 32139 ++++++++++--------- test/data/toxbank-investigation/valid/BII-I-1.rdf | 32139 ++++++++++--------- test/data/toxbank-investigation/valid/BII-I-1.zip | Bin 13225 -> 13684 bytes .../valid/E-MTAB-798_philippe.zip | Bin 111567 -> 111835 bytes test/rdf_check.rb | 40 +- 5 files changed, 34382 insertions(+), 29936 deletions(-) diff --git a/test/data/toxbank-investigation/valid/BII-I-1.n3 b/test/data/toxbank-investigation/valid/BII-I-1.n3 index 6c6fb4a..3ca1c0d 100644 --- a/test/data/toxbank-investigation/valid/BII-I-1.n3 +++ b/test/data/toxbank-investigation/valid/BII-I-1.n3 @@ -1,19648 +1,21871 @@ -@prefix : . +@prefix : . @prefix dc: . @prefix rdfs: . +@prefix tb: . +@prefix foaf: . @prefix isa: . @prefix owl: . @prefix xsd: . @prefix rdf: . @prefix dcterms: . -:MN1290 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.43" ; - isa:hasInputNode :MN735 ; - isa:hasOutputNode :MN396 ; - isa:hasProtocolApplication - :PA2647 ; - isa:hasStudy :S17 . - -:MN2153 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.30" ; - isa:hasInputNode :MN678 ; - isa:hasOutputNode :MN789 ; - isa:hasStudy :S17 . +:DAN405 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.40" ; + isa:hasInputNode :MN2178 ; + isa:hasOutputNode :DN1834 ; + isa:hasStudy :S2 . -:MN795 +:MN1878 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.146:out:0" ; - isa:hasMaterial :M2785 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.29:out:0" ; + isa:hasMaterial :M2234 ; + isa:hasStudy :S2 . -:M2764 +:M2495 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" . - -:DPN1494 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.37" ; - isa:hasInputNode :DN355 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot1" . -:MN1145 +:MN83 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.26" ; - isa:hasInputNode :MN1066 ; - isa:hasOutputNode :MN652 ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.13" ; + isa:hasInputNode :MN1979 ; + isa:hasOutputNode :MN1835 ; isa:hasProtocolApplication - :PA2244 ; - isa:hasStudy :S17 . - -:MN476 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.67:out:0" ; - isa:hasMaterial :M3040 ; - isa:hasStudy :S17 . + :PA2459 ; + isa:hasStudy :S1 . -:DPN1530 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.50" ; - isa:hasInputNode :DN500 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . - -:PA2641 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1129 . +:OE3123 + a isa:OntologyEntry . -:DAN1456 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.80" ; - isa:hasInputNode :MN1103 ; - isa:hasOutputNode :DN564 ; - isa:hasStudy :S17 . +:M3914 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.1-aliquot3" . -:MN1337 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.71" ; - isa:hasInputNode :MN984 ; - isa:hasOutputNode :MN929 ; - isa:hasProtocolApplication - :PA2737 ; - isa:hasStudy :S17 . +:M3763 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.1-aliquot10" . -:DN543 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.29:out:0" ; - isa:hasData :D2977 ; - isa:hasStudy :S17 . +:MN1339 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.13:in:0" ; + isa:hasMaterial :M3693 ; + isa:hasStudy :S2 . -:PA3511 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:MN1443 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.43:out:0" ; + isa:hasMaterial :M3423 ; + isa:hasStudy :S2 . -:M3170 +:M3111 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.07-aliquot1" . - -:PA2368 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC55_Carbon_0.07_External_1_3" . -:MN2009 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.103" ; - isa:hasInputNode :MN572 ; - isa:hasOutputNode :MN443 ; - isa:hasStudy :S17 . +:DPN140 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.7" ; + isa:hasInputNode :DN1352 ; + isa:hasOutputNode :DN1896 ; + isa:hasStudy :S2 . -:MN2154 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.31" ; - isa:hasInputNode :MN678 ; - isa:hasOutputNode :MN789 ; - isa:hasStudy :S17 . +:PA3786 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . -:MN623 +:MN2169 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.79:out:0" ; - isa:hasMaterial :M3502 ; - isa:hasStudy :S17 . - -:M2876 - a isa:Material ; - isa:hasAccessionID "BII-S-2:extract:a_microarray.NZ_4hrs_Drug_Sample_2_Extract" . - -:D3049 - a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC58_Carbon_0.10_External_1_1.txt" . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.3:out:0" ; + isa:hasMaterial :M3401 ; + isa:hasStudy :S2 . -:MN1291 +:MN111 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.161" ; - isa:hasInputNode :MN313 ; - isa:hasOutputNode :MN465 ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.6" ; + isa:hasInputNode :MN1373 ; + isa:hasOutputNode :MN2175 ; isa:hasProtocolApplication - :PA2649 ; - isa:hasStudy :S17 . + :PA2541 ; + 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; - isa:hasInputNode :MN293 ; - isa:hasOutputNode :MN526 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.19" ; + isa:hasInputNode :MN1331 ; + isa:hasOutputNode :MN1389 ; isa:hasProtocolApplication - :PA3477 ; - isa:hasStudy :S17 . + :PA2462 ; + isa:hasStudy :S2 . -:MN1336 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.40" ; - isa:hasInputNode :MN561 ; - isa:hasOutputNode :MN352 ; - isa:hasProtocolApplication - :PA2735 ; - isa:hasStudy :S17 . +:PA3905 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . -:PA3510 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:DPN629 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.47" ; + isa:hasInputNode :DN1538 ; + isa:hasOutputNode :DN2213 ; + isa:hasStudy :S2 . -:D2993 - a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC8_Carbon_0.20_Internal_2_1.txt" . +:OE3199 + a isa:OntologyEntry . -:M2762 +:M2528 a isa:Material ; - 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isa:hasInputNode :DN854 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:A1150 + a isa:Assay . -:MN474 +:MN1444 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.69:in:0" ; - isa:hasMaterial :M3532 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.11:out:0" ; + isa:hasMaterial :M3259 ; + isa:hasStudy :S2 . -:MN849 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.42:out:0" ; - isa:hasMaterial :M2642 ; - isa:hasStudy :S17 . +:DPN416 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.60" ; + isa:hasInputNode :DN1420 ; + isa:hasOutputNode :DN1379 ; + isa:hasStudy :S2 . -:DPN1496 +:DPN141 a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.38" ; - isa:hasInputNode :DN888 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.6" ; + isa:hasInputNode :DN1333 ; + isa:hasOutputNode :DN1714 ; + isa:hasStudy :S2 . 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isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.07-aliquot5" . +:PA2809 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:DPN1468 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.27" ; - isa:hasInputNode :DN680 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1110 + a isa:Protocol ; + rdfs:label "EukGE-WS4"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\EukGE-WS4" ; + dcterms:description "For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip �_� Expression Analysis technical manual. GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5mins, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 �_�l 1x hybridisation buffer and incubated at 45 C for 10 min. 200 �_�l of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1923 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.11" ; - isa:hasInputNode :DN802 ; - isa:hasOutputNode :DN728 ; - isa:hasStudy :S17 . +:D2707 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_derived_data:a_proteome.datatransformation1" ; + isa:hasFactorValue :FV2710 , :FV2709 ; + dcterms:title "datatransformation1" . -:DAN1462 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.78" ; - isa:hasInputNode :MN453 ; - isa:hasOutputNode :DN778 ; - isa:hasStudy :S17 . +:M2681 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3953" . -:D2923 +:D2637 a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC22_Phosphate_0.10_Internal_1_1.txt" . + isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3911" ; + dcterms:title "SCAN:MEXP:3911" . -:MN2216 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.17" ; - isa:hasInputNode :MN756 ; - isa:hasOutputNode :MN1047 ; - isa:hasStudy :S17 . +:MN1959 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16:out:0" ; + isa:hasMaterial :M2452 ; + isa:hasStudy :S2 . -:MN1214 +:MN10 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16" ; - isa:hasInputNode :MN559 ; - isa:hasOutputNode :MN861 ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25" ; + isa:hasInputNode :MN2210 ; + isa:hasOutputNode :MN2103 ; isa:hasProtocolApplication - :PA2449 ; - isa:hasStudy :S17 . - -:MN1856 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.21" ; - isa:hasInputNode :MN762 ; - isa:hasOutputNode :MN834 ; - isa:hasStudy :S17 . + :PA2241 ; + isa:hasStudy :S2 . -:PA3385 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:PA3489 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1112 . -:MN1900 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.41" ; - isa:hasInputNode :MN242 ; - isa:hasOutputNode :MN944 ; - isa:hasStudy :S17 . +:PA2670 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:MN967 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.94:out:0" ; - isa:hasMaterial :M2515 ; - isa:hasStudy :S17 . +:DPN847 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.7" ; + isa:hasInputNode :DN1358 ; + isa:hasOutputNode :DN1585 ; + isa:hasStudy :S2 . -:MN1152 +:MN587 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.0" ; - isa:hasInputNode :MN372 ; - isa:hasOutputNode :MN540 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.37" ; + isa:hasInputNode :MN1927 ; + isa:hasOutputNode :MN1668 ; isa:hasProtocolApplication - :PA2265 ; - isa:hasStudy :S17 . + :PA3455 ; + isa:hasStudy :S2 . -:MN1212 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.14" ; - isa:hasInputNode :MN587 ; - isa:hasOutputNode :MN897 ; - isa:hasProtocolApplication - :PA2443 ; - isa:hasStudy :S17 . +:DAN323 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.81" ; + isa:hasInputNode :MN2034 ; + isa:hasOutputNode :DN1455 ; + isa:hasStudy :S2 . -:MN400 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.91:out:0" ; - isa:hasMaterial :M2765 ; - isa:hasStudy :S17 . +:FV3737 + a isa:FactorValue . -:MN788 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.26:out:0" ; - isa:hasMaterial :M3124 ; - isa:hasStudy :S17 . +:A1310 + a isa:Assay . -:MN2214 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.15" ; - isa:hasInputNode :MN232 ; - isa:hasOutputNode :MN362 ; - isa:hasStudy :S17 . +:P_1111 + a isa:Protocol ; + rdfs:label "growth protocol"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\growth protocol" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:M2479 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot4" . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:M3408 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.07-aliquot5" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorously or 15 s, then 5min incubation at room temperature. -:M2733 +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. + +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl buffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. + +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. + + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . + +:FV3732 + a isa:FactorValue . + +:PA2725 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1103 . + +:M2732 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:G-0.07-aliquot5" . + isa:hasAccessionID "BII-S-1:sample:C-0.07-aliquot6" . -:M2801 +:M2326 a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3922" . + isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot8" . -:PA2226 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . +:DN2062 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.20:out:0" ; + isa:hasData :D3026 ; + isa:hasStudy :S2 . -:DPN1529 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.51" ; - isa:hasInputNode :DN1042 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:OE3546 + a isa:OntologyEntry . -:MN2215 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.16" ; - isa:hasInputNode :MN771 ; - isa:hasOutputNode :MN489 ; - isa:hasStudy :S17 . +:PA2343 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:D3430 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3917" . +:OE3614 + a isa:OntologyEntry . -:MN1211 +:MN588 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.13" ; - isa:hasInputNode :MN455 ; - isa:hasOutputNode :MN553 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.36" ; + isa:hasInputNode :MN1904 ; + isa:hasOutputNode :MN2003 ; isa:hasProtocolApplication - :PA2440 ; - isa:hasStudy :S17 . + :PA3457 ; + isa:hasStudy :S2 . -:MN968 +:MN1672 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.46:out:0" ; - isa:hasMaterial :M2636 ; - isa:hasStudy :S17 . - -:MN1262 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.8" ; - isa:hasInputNode :MN456 ; - isa:hasOutputNode :MN554 ; - isa:hasProtocolApplication - :PA2586 ; - isa:hasStudy :S17 . - -:M2736 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . - -:PA3382 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.74:out:0" ; + isa:hasMaterial :M3482 ; + isa:hasStudy :S2 . -:DPN1466 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.26" ; - isa:hasInputNode :DN222 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1112 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:DPN1812 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.13" ; - isa:hasInputNode :DN713 ; - isa:hasOutputNode :DN600 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:MN765 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.10:out:0" ; - isa:hasMaterial :M2433 ; - isa:hasStudy :S17 . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5min incubation at room temperature. -:DPN1526 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.53" ; - isa:hasInputNode :DN495 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN2218 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.19" ; - isa:hasInputNode :MN252 ; - isa:hasOutputNode :MN255 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:DPN1925 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.12" ; - isa:hasInputNode :DN891 ; - isa:hasOutputNode :DN534 ; - isa:hasStudy :S17 . +7. After precipitation (20 C for 1 h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:DAN1460 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.79" ; - isa:hasInputNode :MN677 ; - isa:hasOutputNode :DN766 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:DN571 +:DN1544 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.8:out:0" ; - isa:hasData :D3058 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.10:out:0" ; + isa:hasData :D3348 ; + isa:hasStudy :S1 . -:MN480 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.75:out:0" ; - isa:hasMaterial :M3237 ; - isa:hasStudy :S17 . +:D2639 + a isa:Data ; + isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3911" ; + isa:hasFactorValue :FV2642 , :FV2641 ; + dcterms:title "SCAN:MEXP:3911" . -:M3406 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.2-aliquot10" . +:OE3271 + a isa:OntologyEntry . -:MN1210 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.12" ; - isa:hasInputNode :MN317 ; - isa:hasOutputNode :MN549 ; - isa:hasProtocolApplication - :PA2437 ; 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+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.68" ; + isa:hasInputNode :MN1471 ; + isa:hasOutputNode :DN2146 ; + isa:hasStudy :S2 . -:PA3579 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:M2813 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" . -:M2699 +:OE3043 + a isa:OntologyEntry . + +:M3833 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot6" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot9" . -:MN559 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.16:out:0" ; - isa:hasMaterial :M2450 ; - isa:hasStudy :S17 . +:I1115 + a isa:Investigation ; + isa:hasAccessionID "BII-I-1" ; + isa:hasOwner :ISA_3977 , :ISA_3976 , :ISA_3975 ; + isa:hasStudy :S1 , :S2 ; + dcterms:abstract """Background +Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. +Results +Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. +Conclusion +This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ; + dcterms:created "29 Apr 2007 20:00:00 GMT" ; + dcterms:issued "9 Mar 2009 21:00:00 GMT" ; + dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" . + +:OE3000 + a isa:OntologyEntry . -:PA3465 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:ProtocolApplication + rdfs:subClassOf isa:Accessible . -:PA3578 +:MN786 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . - -:D2599 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3910" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.49" ; + isa:hasInputNode :MN2174 ; + isa:hasOutputNode :MN2151 ; + isa:hasStudy :S2 . -:D3435 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3918" . +:DPN523 + a isa:DataProcessing ; 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Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. Gene expression at the mRNA level was investigated by transcriptome analysis using Affymetrix hybridization arrays." ; + dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" . -:MN302 +:MN1355 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.40:out:0" ; - isa:hasMaterial :M2331 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.8:out:0" ; + isa:hasMaterial :M2935 ; + isa:hasStudy :S1 . -:M2376 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.2-aliquot6" . +:A1236 + a isa:Assay . -:DPN1625 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.85" ; - isa:hasInputNode :DN482 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:MN2103 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25:out:0" ; + isa:hasMaterial :M2243 ; + isa:hasStudy :S2 . -:M2575 - a isa:Material ; 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- isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.S-0.2-aliquot5" . +:MN1640 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.9:out:0" ; + isa:hasMaterial :M2815 ; + isa:hasStudy :S2 . -:MN1947 +:MN1059 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.55" ; - isa:hasInputNode :MN459 ; - isa:hasOutputNode :MN653 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.2" ; + isa:hasInputNode :MN1782 ; + isa:hasOutputNode :MN1332 ; + isa:hasStudy :S2 . -:MN1004 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.41:out:0" ; - isa:hasMaterial :M2308 ; - isa:hasStudy :S17 . +:MN1000 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.40" ; + isa:hasInputNode :MN2157 ; + isa:hasOutputNode :MN2007 ; + isa:hasStudy :S2 . -:M2432 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_transcriptome.C-0.2-aliquot3" . +:A1192 + a isa:Assay . -:DPN1631 +:DPN496 a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.3" ; - isa:hasInputNode :DN807 ; - isa:hasOutputNode :DN916 ; - isa:hasStudy :S16 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.91" ; + isa:hasInputNode :DN1472 ; + isa:hasOutputNode :DN1379 ; + isa:hasStudy :S2 . -:MN506 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.33:out:0" ; - isa:hasMaterial :M2332 ; - isa:hasStudy :S17 . +:A1191 + a isa:Assay . -:D2969 - a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC38_Ethanol_0.07_Internal_2_1.txt" . +:OE3166 + a isa:OntologyEntry . -:MN1005 +:OE3371 + a isa:OntologyEntry . + +:MN1844 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25:out:0" ; - isa:hasMaterial :M2243 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.15:out:0" ; + isa:hasMaterial :M3263 ; + isa:hasStudy :S2 . -:M3452 +:M2783 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.07-aliquot5" . -:M3077 +:M2578 a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC72_Nitrogen_0.20_External_3_1" . + isa:hasAccessionID "BII-S-1:sample:S-0.07-aliquot7" . -:M2363 +:M3507 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC82_Sulphate_0.07_External_1_3" . -:MN216 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.2.4.3:out:0" ; - isa:hasMaterial :M2402 ; - isa:hasStudy :S16 . +:M3714 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.07-aliquot6" . -:DN258 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.75:out:0" ; - isa:hasData :D3036 ; - isa:hasStudy :S17 . +:DPN404 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.8" ; + isa:hasInputNode :DN1669 ; + isa:hasOutputNode :DN1379 ; + isa:hasStudy :S2 . -:MN1891 +:MN296 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.48" ; - isa:hasInputNode :MN238 ; - isa:hasOutputNode :MN717 ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.9" ; + isa:hasInputNode :MN1790 , :MN1836 , :MN1581 ; + isa:hasOutputNode :MN1640 ; isa:hasProtocolApplication - :PA3398 ; - isa:hasStudy :S17 . + :PA2950 ; + isa:hasStudy :S2 . -:PA2262 +:MN694 a isa:MaterialProcessing ; - isa:hasProtocol :P_1131 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.10" ; + isa:hasInputNode :MN2183 ; + isa:hasOutputNode :MN2114 ; + isa:hasStudy :S2 . -:DAN1843 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.6.7.1" ; - isa:hasInputNode :MN591 ; - isa:hasOutputNode :DN997 ; - isa:hasStudy :S16 . +:DN1797 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.26:out:0" ; + isa:hasData :D3694 ; + isa:hasStudy :S2 . -:DPN1638 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.6" ; - isa:hasInputNode :DN723 ; - isa:hasOutputNode :DN786 ; - isa:hasStudy :S16 . +:MN1058 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.22" ; + isa:hasInputNode :MN1350 ; + isa:hasOutputNode :MN1353 ; + isa:hasStudy :S2 . -:M3517 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.07-aliquot2" . +:DN1716 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.26:out:0" ; + isa:hasData :D3521 ; + isa:hasStudy :S2 . -:D3039 - a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC46_GlucoseO2_0.07_Internal_1_3.txt" . +:OE2987 + a isa:OntologyEntry . -:MN2140 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.65" ; - isa:hasInputNode :MN474 ; - isa:hasOutputNode :MN610 ; - isa:hasProtocolApplication - :PA3547 ; - isa:hasStudy :S17 . +:A1251 + a isa:Assay . -:MN858 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.2:out:0" ; - isa:hasMaterial :M2780 ; - isa:hasStudy :S17 . +:P_1103 + a isa:Protocol ; + rdfs:label "EukGE-WS4"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\EukGE-WS4" ; + dcterms:description "For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip �_� Expression Analysis technical manual. GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5 min, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 ul 1x hybridisation buffer and incubated at 45 C for 10 min. 200 ul of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16 hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1783 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.41" ; - isa:hasInputNode :DN378 ; - isa:hasOutputNode :DN413 ; - isa:hasStudy :S17 . +:M3446 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:P-0.1-aliquot3" . -:M3326 +:M2579 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot7" . -:MN1728 +:PA2518 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . + +:M3506 + a isa:Material ; + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC85_Sulphate_0.10_External_1_1" . + +:PA3917 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . + +:FV3673 + a isa:FactorValue . + +:PA3872 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . + +:MN295 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.26" ; - isa:hasInputNode :MN330 ; - isa:hasOutputNode :MN851 ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.7" ; + isa:hasInputNode :MN1581 ; + isa:hasOutputNode :MN1765 ; isa:hasProtocolApplication - :PA3228 ; - isa:hasStudy :S17 . + :PA2949 ; + isa:hasStudy :S2 . -:MN215 +:MN1841 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.17:out:0" ; - isa:hasMaterial :M3095 ; - isa:hasStudy :S17 . - -:M2364 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.69:out:0" ; + isa:hasMaterial :M3188 ; + isa:hasStudy :S2 . -:MN1890 +:MN693 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.36" ; - isa:hasInputNode :MN931 ; - isa:hasOutputNode :MN793 ; - isa:hasStudy :S17 . - -:M2942 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC50_GlucoseO2_0.10_Internal_2_1" . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.29" ; + isa:hasInputNode :MN1360 ; + isa:hasOutputNode :MN1686 ; + isa:hasProtocolApplication + :PA3657 ; + isa:hasStudy :S2 . -:M3184 - a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot3" . +:A1250 + a isa:Assay . -:DN481 +:DN1501 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.18:out:0" ; - isa:hasData :D2938 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_proteome.7.8.1:out:0" ; + isa:hasData :D2707 ; + isa:hasStudy :S2 . -:PA3415 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:MN1642 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.10:out:0" ; + isa:hasMaterial :M2431 ; + isa:hasStudy :S1 . -:DPN1637 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.7" ; - isa:hasInputNode :DN464 ; - isa:hasOutputNode :DN914 ; - isa:hasStudy :S16 . +:P_1102 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:MN280 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.110:out:0" ; - isa:hasMaterial :M2835 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5 min. -:M2587 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3916" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5 min incubation at room temperature. -:DN537 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.18:out:0" ; - isa:hasData :D3291 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN1729 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.25" ; - isa:hasInputNode :MN610 ; - isa:hasOutputNode :MN383 ; - isa:hasProtocolApplication - :PA3230 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:D3338 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3924" . +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:MN370 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.2:out:0" ; - isa:hasMaterial :M2607 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:M2361 +:MN1057 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.5" ; + isa:hasInputNode :MN1375 ; + isa:hasOutputNode :MN1402 ; + isa:hasStudy :S2 . + +:M2628 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.07-aliquot6" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot6" . -:MN218 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.37:out:0" ; - isa:hasMaterial :M2570 ; - isa:hasStudy :S17 . +:DN1918 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.35:out:0" ; + isa:hasData :D3384 ; + isa:hasStudy :S2 . -:M3001 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC9_Carbon_0.20_Internal_3_1" . +:OE3164 + a isa:OntologyEntry . -:M2771 +:M3712 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.2-aliquot5" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.07-aliquot7" . -:PA3418 - a isa:MaterialProcessing ; 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+ isa:hasStudy :S1 . -:MN712 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.89:out:0" ; - isa:hasMaterial :M3521 ; - isa:hasStudy :S17 . +:PA2405 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . -:MN1090 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.41:out:0" ; - isa:hasMaterial :M2322 ; - isa:hasStudy :S17 . +:M3894 + a isa:Material ; + isa:hasAccessionID "BII-S-1:source:culture16" . +: owl:sameAs :I1115 . diff --git a/test/data/toxbank-investigation/valid/BII-I-1.rdf b/test/data/toxbank-investigation/valid/BII-I-1.rdf index 6c6fb4a..3ca1c0d 100644 --- a/test/data/toxbank-investigation/valid/BII-I-1.rdf +++ b/test/data/toxbank-investigation/valid/BII-I-1.rdf @@ -1,19648 +1,21871 @@ -@prefix : . +@prefix : . @prefix dc: . @prefix rdfs: . +@prefix tb: . +@prefix foaf: . @prefix isa: . @prefix owl: . @prefix xsd: . @prefix rdf: . @prefix dcterms: . -:MN1290 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.43" ; 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- isa:hasData :D3462 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:sample:C-0.1-aliquot6" . -:DN842 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.9:out:0" ; - isa:hasData :D3060 ; - isa:hasStudy :S17 . +:PA3418 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1112 . -:MN269 +:MN1908 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.95:in:0" ; - isa:hasMaterial :M3554 ; - isa:hasStudy :S17 . - -:MN1376 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.94" ; - isa:hasInputNode :MN315 ; - isa:hasOutputNode :MN319 ; - isa:hasProtocolApplication - :PA2821 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.107:out:0" ; + isa:hasMaterial :M3496 ; + isa:hasStudy :S2 . -:M2492 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_transcriptome.N-0.2-aliquot4" . +:PA2778 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:D3367 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3935" . +:FV3801 + a isa:FactorValue . -:M2391 - a isa:Material ; - isa:hasAccessionID "BII-S-2:hybridization:a_microarray.NZ_1hrs_Drug_Sample_1_Labelled_Hyb3" . +:MN904 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.86" ; + isa:hasInputNode :MN1889 ; + isa:hasOutputNode :MN1713 ; + isa:hasStudy :S2 . -:DAN1601 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.21" ; - isa:hasInputNode :MN834 ; - isa:hasOutputNode :DN724 ; - isa:hasStudy :S17 . +:DPN660 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.35" ; + isa:hasInputNode :DN1918 ; + isa:hasOutputNode :DN1693 ; + isa:hasStudy :S2 . -:M3029 +:M2852 a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC63_Carbon_0.20_External_3_1" . + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3920" . -:M3443 - a isa:Material ; - isa:hasAccessionID "BII-S-1:source:culture13" . +:PA3495 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1112 . -:PA3245 +:MN270 a isa:MaterialProcessing ; - isa:hasProtocol :P_1138 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.103" ; + isa:hasInputNode :MN1541 ; + isa:hasOutputNode :MN1459 ; + isa:hasStudy :S2 . -:MN851 +:MN2018 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.26:out:0" ; - isa:hasMaterial :M2488 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.154:out:0" ; + isa:hasMaterial :M2813 ; + isa:hasStudy :S2 . + +:MN1774 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.39:out:0" ; + isa:hasMaterial :M3232 ; + isa:hasStudy :S2 . + +:MN1663 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.27:out:0" ; + isa:hasMaterial :M2712 ; + isa:hasStudy :S2 . + +:MN1550 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.88:out:0" ; + isa:hasMaterial :M3089 ; + isa:hasStudy :S2 . + +isa:appliesProtocol + a owl:FunctionalProperty , owl:ObjectProperty ; + rdfs:domain isa:ProtocolApplication ; + rdfs:range isa:Protocol . -:PA3503 +:OE2995 + a isa:OntologyEntry . + +:MN992 a isa:MaterialProcessing ; 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+ dcterms:title "JIC77_Phosphate_0.10_External_2_1.txt" . + +:DPN138 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.4" ; + isa:hasInputNode :DN1633 ; + isa:hasOutputNode :DN1781 ; + isa:hasStudy :S2 . -:MN791 +:MN1557 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.85:out:0" ; - isa:hasMaterial :M3512 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.55:out:0" ; + isa:hasMaterial :M3838 ; + isa:hasStudy :S2 . -:M2491 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_transcriptome.N-0.2-aliquot4" . +:DAN490 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.16" ; + isa:hasInputNode :MN1416 ; + isa:hasOutputNode :DN1829 ; + isa:hasStudy :S2 . -:PA3500 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:OE2632 + a isa:OntologyEntry . -:MN1377 +:MN886 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.99" ; - isa:hasInputNode :MN825 ; - isa:hasOutputNode :MN326 ; - isa:hasProtocolApplication - :PA2823 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.100" ; + isa:hasInputNode :MN1496 ; + isa:hasOutputNode :MN1440 ; + isa:hasStudy :S2 . -:MN268 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.25:out:0" ; - isa:hasMaterial :M2679 ; - isa:hasStudy :S17 . +:DAN621 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.22" ; + isa:hasInputNode :MN2219 ; + isa:hasOutputNode :DN1403 ; + isa:hasStudy :S2 . -:MN2008 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.153" ; - isa:hasInputNode :MN283 ; - isa:hasOutputNode :MN236 ; - isa:hasProtocolApplication - :PA3503 ; - isa:hasStudy :S17 . +:MN1882 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.24:out:0" ; + isa:hasMaterial :M2240 ; + isa:hasStudy :S2 . -:PA2652 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:DN2185 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.73:out:0" ; 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- isa:hasStudy :S17 . +:MN1670 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.103:out:0" ; + isa:hasMaterial :M2976 ; + isa:hasStudy :S2 . -:MN966 +:OE3616 + a isa:OntologyEntry . + +:D3163 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC63_Carbon_0.20_External_3_1.txt" ; + dcterms:title "JIC63_Carbon_0.20_External_3_1.txt" . + +:MN1898 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.9:out:0" ; - isa:hasMaterial :M2547 ; - isa:hasStudy :S16 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.12:out:0" ; + isa:hasMaterial :M3395 ; + isa:hasStudy :S2 . -:DPN1528 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.52" ; - isa:hasInputNode :DN385 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:DN1753 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.14:out:0" ; + isa:hasData :D3542 ; + isa:hasStudy :S2 . -:M2734 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.07-aliquot5" . +:PA2809 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:DPN1468 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.27" ; - isa:hasInputNode :DN680 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1110 + a isa:Protocol ; + rdfs:label "EukGE-WS4"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\EukGE-WS4" ; + dcterms:description "For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip �_� Expression Analysis technical manual. GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5mins, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 �_�l 1x hybridisation buffer and incubated at 45 C for 10 min. 200 �_�l of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1923 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.11" ; - isa:hasInputNode :DN802 ; - isa:hasOutputNode :DN728 ; - isa:hasStudy :S17 . +:D2707 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_derived_data:a_proteome.datatransformation1" ; + isa:hasFactorValue :FV2710 , :FV2709 ; + dcterms:title "datatransformation1" . -:DAN1462 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.78" ; - isa:hasInputNode :MN453 ; - isa:hasOutputNode :DN778 ; - isa:hasStudy :S17 . +:M2681 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3953" . -:D2923 +:D2637 a isa:Data ; - isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC22_Phosphate_0.10_Internal_1_1.txt" . + isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3911" ; + dcterms:title "SCAN:MEXP:3911" . -:MN2216 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.17" ; - isa:hasInputNode :MN756 ; - isa:hasOutputNode :MN1047 ; - isa:hasStudy :S17 . +:MN1959 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16:out:0" ; + isa:hasMaterial :M2452 ; + isa:hasStudy :S2 . -:MN1214 +:MN10 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.16" ; - isa:hasInputNode :MN559 ; - isa:hasOutputNode :MN861 ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25" ; + isa:hasInputNode :MN2210 ; + isa:hasOutputNode :MN2103 ; isa:hasProtocolApplication - :PA2449 ; - isa:hasStudy :S17 . - -:MN1856 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.21" ; - isa:hasInputNode :MN762 ; - isa:hasOutputNode :MN834 ; - isa:hasStudy :S17 . + :PA2241 ; + isa:hasStudy :S2 . -:PA3385 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:PA3489 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1112 . -:MN1900 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.41" ; - isa:hasInputNode :MN242 ; - isa:hasOutputNode :MN944 ; - isa:hasStudy :S17 . +:PA2670 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:MN967 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.94:out:0" ; - isa:hasMaterial :M2515 ; - isa:hasStudy :S17 . +:DPN847 + a isa:DataProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.7" ; + isa:hasInputNode :DN1358 ; + isa:hasOutputNode :DN1585 ; + isa:hasStudy :S2 . -:MN1152 +:MN587 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.0" ; - isa:hasInputNode :MN372 ; - isa:hasOutputNode :MN540 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.37" ; + isa:hasInputNode :MN1927 ; + isa:hasOutputNode :MN1668 ; isa:hasProtocolApplication - :PA2265 ; - isa:hasStudy :S17 . + :PA3455 ; + isa:hasStudy :S2 . -:MN1212 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.14" ; - isa:hasInputNode :MN587 ; - isa:hasOutputNode :MN897 ; - isa:hasProtocolApplication - :PA2443 ; - isa:hasStudy :S17 . +:DAN323 + a isa:DataAcquisition ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.81" ; + isa:hasInputNode :MN2034 ; + isa:hasOutputNode :DN1455 ; + isa:hasStudy :S2 . -:MN400 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.91:out:0" ; - isa:hasMaterial :M2765 ; - isa:hasStudy :S17 . +:FV3737 + a isa:FactorValue . -:MN788 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.26:out:0" ; - isa:hasMaterial :M3124 ; - isa:hasStudy :S17 . +:A1310 + a isa:Assay . -:MN2214 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.15" ; - isa:hasInputNode :MN232 ; - isa:hasOutputNode :MN362 ; - isa:hasStudy :S17 . +:P_1111 + a isa:Protocol ; + rdfs:label "growth protocol"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\growth protocol" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:M2479 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot4" . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:M3408 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.07-aliquot5" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorously or 15 s, then 5min incubation at room temperature. -:M2733 +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. + +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl buffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. + +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. + + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . + +:FV3732 + a isa:FactorValue . + +:PA2725 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1103 . + +:M2732 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:G-0.07-aliquot5" . + isa:hasAccessionID "BII-S-1:sample:C-0.07-aliquot6" . -:M2801 +:M2326 a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3922" . + isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot8" . -:PA2226 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1133 . +:DN2062 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.20:out:0" ; + isa:hasData :D3026 ; + isa:hasStudy :S2 . -:DPN1529 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.51" ; - isa:hasInputNode :DN1042 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:OE3546 + a isa:OntologyEntry . -:MN2215 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.16" ; - isa:hasInputNode :MN771 ; - isa:hasOutputNode :MN489 ; - isa:hasStudy :S17 . +:PA2343 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . -:D3430 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3917" . +:OE3614 + a isa:OntologyEntry . -:MN1211 +:MN588 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.13" ; - isa:hasInputNode :MN455 ; - isa:hasOutputNode :MN553 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.36" ; + isa:hasInputNode :MN1904 ; + isa:hasOutputNode :MN2003 ; isa:hasProtocolApplication - :PA2440 ; - isa:hasStudy :S17 . + :PA3457 ; + isa:hasStudy :S2 . -:MN968 +:MN1672 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.46:out:0" ; - isa:hasMaterial :M2636 ; - isa:hasStudy :S17 . - -:MN1262 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.8" ; - isa:hasInputNode :MN456 ; - isa:hasOutputNode :MN554 ; - isa:hasProtocolApplication - :PA2586 ; - isa:hasStudy :S17 . - -:M2736 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . - -:PA3382 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.74:out:0" ; + isa:hasMaterial :M3482 ; + isa:hasStudy :S2 . -:DPN1466 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.26" ; - isa:hasInputNode :DN222 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:P_1112 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-1\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:DPN1812 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.13" ; - isa:hasInputNode :DN713 ; - isa:hasOutputNode :DN600 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. -:MN765 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.10:out:0" ; - isa:hasMaterial :M2433 ; - isa:hasStudy :S17 . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5min incubation at room temperature. -:DPN1526 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.53" ; - isa:hasInputNode :DN495 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN2218 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.19" ; - isa:hasInputNode :MN252 ; - isa:hasOutputNode :MN255 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:DPN1925 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.12" ; - isa:hasInputNode :DN891 ; - isa:hasOutputNode :DN534 ; - isa:hasStudy :S17 . +7. After precipitation (20 C for 1 h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:DAN1460 - a isa:DataAcquisition ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.79" ; - isa:hasInputNode :MN677 ; - isa:hasOutputNode :DN766 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:DN571 +:DN1544 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.8:out:0" ; - isa:hasData :D3058 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.10:out:0" ; + isa:hasData :D3348 ; + isa:hasStudy :S1 . -:MN480 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.75:out:0" ; - isa:hasMaterial :M3237 ; - isa:hasStudy :S17 . +:D2639 + a isa:Data ; + isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3911" ; + isa:hasFactorValue :FV2642 , :FV2641 ; + dcterms:title "SCAN:MEXP:3911" . -:M3406 - a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.2-aliquot10" . +:OE3271 + a isa:OntologyEntry . -:MN1210 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.12" ; - isa:hasInputNode :MN317 ; - isa:hasOutputNode :MN549 ; - isa:hasProtocolApplication - :PA2437 ; - isa:hasStudy :S17 . +:D3160 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC69_Nitrogen_0.10_External_3_1.txt" ; + dcterms:title "JIC69_Nitrogen_0.10_External_3_1.txt" . -:MN1854 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.26" ; - isa:hasInputNode :MN753 ; - isa:hasOutputNode :MN788 ; - isa:hasStudy :S17 . +:ISA_1113 + a foaf:Person , isa:Contact ; + foaf:family_name "Leo"^^xsd:string ; + foaf:givenname "Zeef"^^xsd:string . + +:MN1895 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.59:out:0" ; + isa:hasMaterial :M3822 ; + isa:hasStudy :S2 . -:MN764 +:MN1671 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.36:out:0" ; - isa:hasMaterial :M2317 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.66:out:0" ; + isa:hasMaterial :M2733 ; + isa:hasStudy :S2 . -:MN1150 +:MN589 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.21" ; 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+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.68" ; + isa:hasInputNode :MN1471 ; + isa:hasOutputNode :DN2146 ; + isa:hasStudy :S2 . -:PA3579 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:M2813 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" . -:M2699 +:OE3043 + a isa:OntologyEntry . + +:M3833 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot6" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot9" . -:MN559 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.16:out:0" ; - isa:hasMaterial :M2450 ; - isa:hasStudy :S17 . +:I1115 + a isa:Investigation ; + isa:hasAccessionID "BII-I-1" ; + isa:hasOwner :ISA_3977 , :ISA_3976 , :ISA_3975 ; + isa:hasStudy :S1 , :S2 ; + dcterms:abstract """Background +Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. +Results +Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. +Conclusion +This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ; + dcterms:created "29 Apr 2007 20:00:00 GMT" ; + dcterms:issued "9 Mar 2009 21:00:00 GMT" ; + dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" . + +:OE3000 + a isa:OntologyEntry . -:PA3465 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:ProtocolApplication + rdfs:subClassOf isa:Accessible . -:PA3578 +:MN786 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . - -:D2599 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_raw_data:a_transcriptome.SCAN:MEXP:3910" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.49" ; + isa:hasInputNode :MN2174 ; + isa:hasOutputNode :MN2151 ; + isa:hasStudy :S2 . -:D3435 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3918" . +:DPN523 + a isa:DataProcessing ; 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To achieve this, we carried out our analyses on yeast grown in steady-state chemostat culture under four different nutrient limitations (glucose, ammonium, phosphate, and sulfate) at three different dilution (that is, growth) rates (D = u = 0.07, 0.1, and 0.2/hour, equivalent to population doubling times (Td) of 10 hours, 7 hours, and 3.5 hours, respectively; u = specific growth rate defined as grams of biomass generated per gram of biomass present per unit time)." ; + dcterms:title "Study of the impact of changes in flux on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae under different nutrient limitations" . -:M3525 +:M2357 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.1-aliquot3" . + isa:hasAccessionID "BII-S-2:sample:NZ_0hrs_Grow_2" . -:MN670 +:MN1629 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.61:out:0" ; - isa:hasMaterial :M3471 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.73:out:0" ; 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Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. Gene expression at the mRNA level was investigated by transcriptome analysis using Affymetrix hybridization arrays." ; + dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" . -:MN302 +:MN1355 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.40:out:0" ; - isa:hasMaterial :M2331 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.8:out:0" ; + isa:hasMaterial :M2935 ; + isa:hasStudy :S1 . -:M2376 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.2-aliquot6" . +:A1236 + a isa:Assay . -:DPN1625 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.85" ; - isa:hasInputNode :DN482 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:MN2103 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.25:out:0" ; + isa:hasMaterial :M2243 ; + isa:hasStudy :S2 . -:M2575 - a isa:Material ; 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GeneChip �_� control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip �_� manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5 min, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 ul 1x hybridisation buffer and incubated at 45 C for 10 min. 200 ul of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16 hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software." . -:DPN1783 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.41" ; - isa:hasInputNode :DN378 ; - isa:hasOutputNode :DN413 ; - isa:hasStudy :S17 . +:M3446 + a isa:Material ; + isa:hasAccessionID "BII-S-1:sample:P-0.1-aliquot3" . -:M3326 +:M2579 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot7" . -:MN1728 +:PA2518 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1107 . + +:M3506 + a isa:Material ; + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC85_Sulphate_0.10_External_1_1" . + +:PA3917 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . + +:FV3673 + a isa:FactorValue . + +:PA3872 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1111 . + +:MN295 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.26" ; - isa:hasInputNode :MN330 ; - isa:hasOutputNode :MN851 ; + isa:hasAccessionID "BII-S-1:proc:a_proteome.2.4.7" ; + isa:hasInputNode :MN1581 ; + isa:hasOutputNode :MN1765 ; isa:hasProtocolApplication - :PA3228 ; - isa:hasStudy :S17 . + :PA2949 ; + isa:hasStudy :S2 . -:MN215 +:MN1841 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.17:out:0" ; - isa:hasMaterial :M3095 ; - isa:hasStudy :S17 . - -:M2364 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot9" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.69:out:0" ; + isa:hasMaterial :M3188 ; + isa:hasStudy :S2 . -:MN1890 +:MN693 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.36" ; - isa:hasInputNode :MN931 ; - isa:hasOutputNode :MN793 ; - isa:hasStudy :S17 . - -:M2942 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC50_GlucoseO2_0.10_Internal_2_1" . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.29" ; + isa:hasInputNode :MN1360 ; + isa:hasOutputNode :MN1686 ; + isa:hasProtocolApplication + :PA3657 ; + isa:hasStudy :S2 . -:M3184 - a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot3" . +:A1250 + a isa:Assay . -:DN481 +:DN1501 a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.18:out:0" ; - isa:hasData :D2938 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_proteome.7.8.1:out:0" ; + isa:hasData :D2707 ; + isa:hasStudy :S2 . -:PA3415 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +:MN1642 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.10:out:0" ; + isa:hasMaterial :M2431 ; + isa:hasStudy :S1 . -:DPN1637 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.7" ; - isa:hasInputNode :DN464 ; - isa:hasOutputNode :DN914 ; - isa:hasStudy :S16 . +:P_1102 + a isa:Protocol ; + rdfs:label "mRNA extraction"^^xsd:string ; + isa:hasAccessionID "BII-S-2\\mRNA extraction" ; + dcterms:description """1. Biomass samples (45ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) -:MN280 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.110:out:0" ; - isa:hasMaterial :M2835 ; - isa:hasStudy :S17 . +2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5 min. -:M2587 - a isa:Material ; - isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3916" . +3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5 min incubation at room temperature. -:DN537 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.18:out:0" ; - isa:hasData :D3291 ; - isa:hasStudy :S17 . +4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. +5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. -:MN1729 - a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.25" ; - isa:hasInputNode :MN610 ; - isa:hasOutputNode :MN383 ; - isa:hasProtocolApplication - :PA3230 ; - isa:hasStudy :S17 . +6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. -:D3338 - a isa:Data ; - isa:hasAccessionID "BII-S-1:microarray_normalized_data:a_transcriptome.SCAN:MEXP:3924" . +7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. -:MN370 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.2:out:0" ; - isa:hasMaterial :M2607 ; - isa:hasStudy :S17 . + 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" . -:M2361 +:MN1057 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.5" ; + isa:hasInputNode :MN1375 ; + isa:hasOutputNode :MN1402 ; + isa:hasStudy :S2 . + +:M2628 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.N-0.07-aliquot6" . + isa:hasAccessionID "BII-S-1:extract:a_metabolome.S-0.07-aliquot6" . -:MN218 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.37:out:0" ; - isa:hasMaterial :M2570 ; - isa:hasStudy :S17 . +:DN1918 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.35:out:0" ; + isa:hasData :D3384 ; + isa:hasStudy :S2 . -:M3001 - a isa:Material ; - isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC9_Carbon_0.20_Internal_3_1" . +:OE3164 + a isa:OntologyEntry . -:M2771 +:M3712 a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_metabolome.G-0.2-aliquot5" . + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.P-0.07-aliquot7" . -:PA3418 - a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . +isa:hasProtocolApplication + a owl:ObjectProperty ; + rdfs:domain isa:Processing ; + rdfs:range isa:ProtocolApplication . -:DPN1636 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.7.8.8" ; - isa:hasInputNode :DN297 ; - isa:hasOutputNode :DN744 ; - isa:hasStudy :S16 . +:FV3672 + a isa:FactorValue . -:M3515 +:M3505 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.2-aliquot4" . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC86_Sulphate_0.10_External_2_1" . -:MN371 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:s_BII-S-2.0.2.0:in:0" ; - isa:hasMaterial :M2355 ; - isa:hasStudy :S16 . +:M2785 + a isa:Material ; + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3948" . -:M3186 +:OE3586 + a isa:OntologyEntry . + +:FV3662 + a isa:FactorValue . + +:M2775 a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.1-aliquot4" . + isa:hasAccessionID "BII-S-1:hybridization:a_transcriptome.HYB:MEXP:3942" . + +:DN1709 + a isa:DataNode ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.30:out:0" ; + isa:hasData :D3725 ; + isa:hasStudy :S2 . -:MN217 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.38:out:0" ; - isa:hasMaterial :M2707 ; - isa:hasStudy :S17 . +:D3119 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC16_Nitrogen_0.20_Internal_1_1.txt" ; + dcterms:title "JIC16_Nitrogen_0.20_Internal_1_1.txt" . -:MN282 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_proteome.4.5.2:out:0" ; - isa:hasMaterial :M2759 ; - isa:hasStudy :S17 . +:FV2968 + a isa:FactorValue . -:M2418 - a isa:Material ; - isa:hasAccessionID "BII-S-1:extract:a_proteome.N-0.2" . +:OE2990 + a isa:OntologyEntry . -:DPN1635 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.90" ; - isa:hasInputNode :DN886 ; - isa:hasOutputNode :DN281 ; - isa:hasStudy :S17 . +:FV3708 + a isa:FactorValue . -:MN449 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.7:out:0" ; - isa:hasMaterial :M2285 ; - isa:hasStudy :S17 . +:A1196 + a isa:Assay . -:PA3417 +:MN1004 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . + isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.62" ; + isa:hasInputNode :MN1357 ; + isa:hasOutputNode :MN1974 ; + isa:hasProtocolApplication + :PA3934 ; + isa:hasStudy :S2 . -:DN535 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.6.7.4:out:0" ; - isa:hasData :D2608 ; - isa:hasStudy :S17 . +:PA2402 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1110 . -:PA3341 +:MN964 a isa:MaterialProcessing ; - isa:hasProtocol :P_1137 . - -:MN859 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.7:out:0" ; - isa:hasMaterial :M2381 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.63" ; + isa:hasInputNode :MN1967 ; + isa:hasOutputNode :MN1798 ; + isa:hasStudy :S2 . -:MN1895 +:MN285 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.53" ; - isa:hasInputNode :MN259 ; - isa:hasOutputNode :MN665 ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.8" ; + isa:hasInputNode :MN1704 ; + isa:hasOutputNode :MN1355 ; isa:hasProtocolApplication - :PA3403 ; - isa:hasStudy :S17 . + :PA2934 ; + isa:hasStudy :S1 . -:DN534 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.12:out:0" ; - isa:hasData :D3432 ; - isa:hasStudy :S17 . +:MN1851 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.26:out:0" ; + isa:hasMaterial :M3710 ; + isa:hasStudy :S2 . -:DN484 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.109:out:0" ; - isa:hasData :D3466 ; - isa:hasStudy :S17 . +:MN2119 + a isa:MaterialNode ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.98:out:0" ; + isa:hasMaterial :M3061 ; + isa:hasStudy :S2 . -:PA2867 +:D3834 + a isa:Data ; + isa:hasAccessionID "BII-S-1:ms_spec_raw_data:a_metabolome.JIC91_Ethanol_0.07_External_1_1.txt" ; + dcterms:title "JIC91_Ethanol_0.07_External_1_1.txt" . + +:MN59 a isa:MaterialProcessing ; - isa:hasProtocol :P_1128 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.0" ; + isa:hasInputNode :MN1988 ; + isa:hasOutputNode :MN1583 ; + isa:hasProtocolApplication + :PA2387 ; + isa:hasStudy :S1 . -:DPN1572 - 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isa:hasAccessionID "BII-S-1:extract:a_metabolome.C-0.1-aliquot10" . + isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC49_GlucoseO2_0.10_Internal_1_1" . -:MN1896 +:MN286 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.56" ; - isa:hasInputNode :MN259 ; - isa:hasOutputNode :MN231 ; + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.7" ; + isa:hasInputNode :MN1704 ; + isa:hasOutputNode :MN1637 ; isa:hasProtocolApplication - :PA3404 ; - isa:hasStudy :S17 . + :PA2936 ; + isa:hasStudy :S1 . -:MN1724 +:MN965 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.39" ; - isa:hasInputNode :MN796 ; - isa:hasOutputNode :MN1079 ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.62" ; + isa:hasInputNode :MN2112 ; + isa:hasOutputNode :MN1365 ; + isa:hasStudy :S2 . + +:OE3582 + a isa:OntologyEntry . + +:M3891 + a isa:Material ; + isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.1-aliquot4" . + +:MN58 + a isa:MaterialProcessing ; + isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.55" ; + isa:hasInputNode :MN1977 ; + isa:hasOutputNode :MN1786 ; isa:hasProtocolApplication - 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isa:hasProtocol :P_1137 . - -:MN927 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.45:out:0" ; - isa:hasMaterial :M3186 ; - isa:hasStudy :S17 . - -:MN664 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.11:out:0" ; - isa:hasMaterial :M3156 ; - isa:hasStudy :S17 . - -:MN511 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.72:out:0" ; - isa:hasMaterial :M2748 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.8" ; + isa:hasInputNode :MN1386 ; + isa:hasOutputNode :MN1912 ; + isa:hasProtocolApplication + :PA3404 ; + isa:hasStudy :S2 . -:MN926 +:MN1348 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.12:out:0" ; - isa:hasMaterial :M2424 ; - isa:hasStudy :S16 . - -:DN427 - a isa:DataNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.84:out:0" ; - isa:hasData :D2931 ; - isa:hasStudy :S17 . - -:M3223 - a isa:Material ; - isa:hasAccessionID "BII-S-1:sample:N-0.2-aliquot3" . + isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.13:out:0" ; + isa:hasMaterial :M3644 ; + isa:hasStudy :S2 . -:MN1223 +:MN179 a isa:MaterialProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.29" ; - isa:hasInputNode :MN404 ; - isa:hasOutputNode :MN864 ; + isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.25" ; + isa:hasInputNode :MN1540 ; + isa:hasOutputNode :MN1366 ; isa:hasProtocolApplication - :PA2475 ; - isa:hasStudy :S17 . + :PA2727 ; + isa:hasStudy :S2 . -:M3449 +:M2364 a isa:Material ; - isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot8" . + isa:hasAccessionID "BII-S-1:sample:C-0.1-aliquot9" . -:MN860 +:MN1349 a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.71:out:0" ; - isa:hasMaterial :M2497 ; - isa:hasStudy :S17 . - -:DPN1976 - a isa:DataProcessing ; - isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.9" ; - isa:hasInputNode :DN260 ; - isa:hasOutputNode :DN487 ; - isa:hasStudy :S17 . + isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.13:out:0" ; + isa:hasMaterial :M2466 ; + isa:hasStudy :S1 . -:MN712 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.89:out:0" ; - isa:hasMaterial :M3521 ; - isa:hasStudy :S17 . +:PA2405 + a isa:ProtocolApplication ; + isa:appliesProtocol :P_1109 . -:MN1090 - a isa:MaterialNode ; - isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.41:out:0" ; - isa:hasMaterial :M2322 ; - isa:hasStudy :S17 . +:M3894 + a isa:Material ; + isa:hasAccessionID "BII-S-1:source:culture16" . +: owl:sameAs :I1115 . diff --git a/test/data/toxbank-investigation/valid/BII-I-1.zip b/test/data/toxbank-investigation/valid/BII-I-1.zip index fa56e5a..fbe4cdf 100644 Binary files a/test/data/toxbank-investigation/valid/BII-I-1.zip and b/test/data/toxbank-investigation/valid/BII-I-1.zip differ diff --git a/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip b/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip index c1aa89c..d0d0ffe 100644 Binary files a/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip and b/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip differ diff --git a/test/rdf_check.rb b/test/rdf_check.rb index 587e342..c6de5ce 100644 --- a/test/rdf_check.rb +++ b/test/rdf_check.rb @@ -10,37 +10,37 @@ class UploadTest < Test::Unit::TestCase def test_01_check_rdf_with_ToxBank_specific_fields_on_BII_I_1 id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp assert_match /[Investigation Identifier, BII\-I\-1]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Owning Organisation URI, TBO\:G176]/, response - #test_id_query_sparqle - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Consortium URI, TBC:G2]/, response - #test_resource_ISA - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + assert_match /[Consortium URI, TBC\:G2, Douglas Connect]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + assert_match /[Principal Investigator URI, TBU\:U115, Glenn Myatt]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response end def test_02_check_rdf_with_ToxBank_specific_fields_on_E_MTAB id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp assert_match /[Investigation Identifier, E\-MTAB\-798]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp assert_match /[Investigation Title, Open TG\-GATEs \(in vitro, human\)]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp assert_match /[Investigation Description, The Toxicogenomics Project was a 5\-year collaborative project]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Owning Organisation URI, TBO\:G176]/, response - #test_id_query_sparqle - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Consortium URI, TBC:G2]/, response - #test_resource_ISA - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + assert_match /[Consortium URI, TBC:G2, Douglas Connect]/, response + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp assert_match /[Investigation keywords, TBK\:Fluxomics]/, response end -- cgit v1.2.3 From ed29318710436187d7b8de5e4a18f954ab640d5d Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 11:43:38 +0200 Subject: changed uri --- test/rdf_check.rb | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/test/rdf_check.rb b/test/rdf_check.rb index c6de5ce..d8838a5 100644 --- a/test/rdf_check.rb +++ b/test/rdf_check.rb @@ -10,37 +10,37 @@ class UploadTest < Test::Unit::TestCase def test_01_check_rdf_with_ToxBank_specific_fields_on_BII_I_1 id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation Identifier, BII\-I\-1]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Consortium URI, TBC\:G2, Douglas Connect]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Principal Investigator URI, TBU\:U115, Glenn Myatt]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response end def test_02_check_rdf_with_ToxBank_specific_fields_on_E_MTAB id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Investigation Identifier, E\-MTAB\-798]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Investigation Title, Open TG\-GATEs \(in vitro, human\)]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Investigation Description, The Toxicogenomics Project was a 5\-year collaborative project]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Consortium URI, TBC:G2, Douglas Connect]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/2`.chomp + response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp assert_match /[Investigation keywords, TBK\:Fluxomics]/, response end -- cgit v1.2.3 From 15c8e87680f380a818b5e834f45b89d37daccd16 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 16:55:18 +0200 Subject: include rdf_check --- test/toxbank-investigation-rest.rb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/test/toxbank-investigation-rest.rb b/test/toxbank-investigation-rest.rb index 3e1b295..a269216 100644 --- a/test/toxbank-investigation-rest.rb +++ b/test/toxbank-investigation-rest.rb @@ -43,6 +43,16 @@ class BasicTestCRUDInvestigation < Test::Unit::TestCase uri = task.resultURI @@uri = URI(uri) assert @@uri.host == URI($toxbank_investigation[:uri]).host + # check_rdf + response = `curl -i -k -H subjectid:#{@@subjectid} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response + assert_match /[Investigation Identifier, BII\-I\-1]/, response + assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response + assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response + assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response + assert_match /[Consortium URI, TBC\:G2, Douglas Connect]/, response + assert_match /[Principal Investigator URI, TBU\:U115, Glenn Myatt]/, response + assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response end # get investigation/{id} as text/uri-list -- cgit v1.2.3 From d38ccfed10c176b457890037e8fcc4d9b7760322 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 16:55:36 +0200 Subject: add urilist --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index d87d4be..aaffbb3 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,4 @@ spec/reports test/tmp test/version_tmp tmp +/test/urilist.rb -- cgit v1.2.3 From 6596ff877e655433ff42d9c1c785bb4c71eb244a Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 16:57:15 +0200 Subject: remove rdf_check --- test/rdf_check.rb | 47 ----------------------------------------------- 1 file changed, 47 deletions(-) delete mode 100644 test/rdf_check.rb diff --git a/test/rdf_check.rb b/test/rdf_check.rb deleted file mode 100644 index d8838a5..0000000 --- a/test/rdf_check.rb +++ /dev/null @@ -1,47 +0,0 @@ -require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb") - -class UploadTest < Test::Unit::TestCase - - def setup - end - - def teardown - end - - def test_01_check_rdf_with_ToxBank_specific_fields_on_BII_I_1 - id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Investigation Identifier, BII\-I\-1]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Consortium URI, TBC\:G2, Douglas Connect]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Principal Investigator URI, TBU\:U115, Glenn Myatt]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/0`.chomp - assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response - end - - def test_02_check_rdf_with_ToxBank_specific_fields_on_E_MTAB - id = OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Investigation Identifier, E\-MTAB\-798]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Investigation Title, Open TG\-GATEs \(in vitro, human\)]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Investigation Description, The Toxicogenomics Project was a 5\-year collaborative project]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Consortium URI, TBC:G2, Douglas Connect]/, response - response = `curl -i -k -H subjectid:#{id} -H accept:application/rdf+xml https://toxbank-dev.in-silico.ch/2`.chomp - assert_match /[Investigation keywords, TBK\:Fluxomics]/, response - end - -end -- cgit v1.2.3 From 22fa8d86e8975458e887ca176097bfe7c4f5a28c Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 17:06:45 +0200 Subject: added variable uri --- test/toxbank-investigation-rest.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/toxbank-investigation-rest.rb b/test/toxbank-investigation-rest.rb index a269216..5421972 100644 --- a/test/toxbank-investigation-rest.rb +++ b/test/toxbank-investigation-rest.rb @@ -44,7 +44,7 @@ class BasicTestCRUDInvestigation < Test::Unit::TestCase @@uri = URI(uri) assert @@uri.host == URI($toxbank_investigation[:uri]).host # check_rdf - response = `curl -i -k -H subjectid:#{@@subjectid} -H accept:application/rdf+xml #{$toxbank_investigation[:uri]}/0`.chomp + response = `curl -i -k -H subjectid:#{@@subjectid} -H accept:application/rdf+xml #{uri}`.chomp assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response assert_match /[Investigation Identifier, BII\-I\-1]/, response assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response -- cgit v1.2.3 From 81346e1ba9624b57e476688167157e64e07c60fd Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 7 May 2012 17:27:25 +0200 Subject: removed isa-tab-renamed.zip --- .../toxbank-investigation/valid/isa-tab-renamed.zip | Bin 15666 -> 0 bytes test/toxbank-investigation-curl.rb | 7 +++---- 2 files changed, 3 insertions(+), 4 deletions(-) delete mode 100644 test/data/toxbank-investigation/valid/isa-tab-renamed.zip diff --git a/test/data/toxbank-investigation/valid/isa-tab-renamed.zip b/test/data/toxbank-investigation/valid/isa-tab-renamed.zip deleted file mode 100644 index b8130a8..0000000 Binary files a/test/data/toxbank-investigation/valid/isa-tab-renamed.zip and /dev/null differ diff --git a/test/toxbank-investigation-curl.rb b/test/toxbank-investigation-curl.rb index f228bb4..2810103 100644 --- a/test/toxbank-investigation-curl.rb +++ b/test/toxbank-investigation-curl.rb @@ -24,8 +24,7 @@ class UploadTest < Test::Unit::TestCase def test_03_valid_zip_upload # upload - #["E-MTAB-798_philippe.zip"].each do |f| - ["BII-I-1.zip","isa-tab-renamed.zip","E-MTAB-798_philippe.zip"].each do |f| + ["BII-I-1.zip","E-MTAB-798_philippe.zip"].each do |f| file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f response = `curl -Lk -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{@@subjectid}" #{$toxbank_investigation[:uri]}`.chomp assert_match /202/, response @@ -73,7 +72,7 @@ class UploadTest < Test::Unit::TestCase =begin def test_rest_client_wrapper - ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f| + ["BII-I-1.zip"].each do |f| file = File.join File.dirname(__FILE__), "toxbank-investigation","data/toxbank-investigation/valid", f investigation_uri = OpenTox::RestClientWrapper.post $toxbank_investigation[:uri], {:file => File.read(file),:name => file}, {:content_type => "application/zip", :subjectid => @@subjectid} puts investigation_uri @@ -103,7 +102,7 @@ class UploadTest < Test::Unit::TestCase =begin def test_ruby_api - ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f| + ["BII-I-1.zip"].each do |f| file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f investigation = OpenTox::Investigation.create $toxbank_investigation[:uri], :file => file, :headers => {:content_type => "application/zip", :subjectid => @@subjectid} zip = File.join @tmpdir,"tmp.zip" -- cgit v1.2.3