toxbank-investigation 0.0.1pre-x86-linux

data/README

@@ -0,0 +1,14 @@
+toxbank-investigation: Investigation service for ToxBank
+
+Installation:
+
+  Dependencies: ruby 1.9.x, git, zip, java, curl, wget
+
+  gem install toxbank-investigation
+  toxbank-investigation-install # service setup, configuration and webserver start
+
+Development:
+
+  see https://github.com/opentox/opentox-server
+  
+ 

data/Rakefile

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+require "bundler/gem_tasks"
+require 'bundler'
+Bundler.require
+Bundler.setup
+
+# TODO: pass constants to test files
+require File.join(ENV["HOME"],".opentox","config","toxbank-investigation","production.rb")
+# TODO: autostart unicorn??
+HOST = "http://localhost:8080"
+
+
+require 'rake/testtask'
+task :setup do
+  # setup code
+  if AA_SERVER
+    resource = RestClient::Resource.new("#{AA_SERVER}/auth/authenticate")
+    @@subjectid = resource.post(:username=>TEST_USER, :password => TEST_PW).sub("token.id=","").sub("\n","")
+  else
+    @@subjectid = ""
+  end
+end
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+  t.test_files = FileList['test/upload.rb']
+  #t.test_files = FileList['test/*.rb']
+  t.verbose = true
+end
+
+desc "Run tests"
+task :default => :test

data/application.rb

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+require "opentox-server"
+require File.join(ENV["HOME"],".opentox","config","toxbank-investigation","production.rb")
+
+
+module OpenTox
+  class Application < Service
+
+    helpers do
+
+      def uri
+        params[:id] ? url_for("/#{params[:id]}", :full) : "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
+      end
+
+      def uri_list 
+        params[:id] ? d = "./investigation/#{params[:id]}/*" : d = "./investigation/*"
+        Dir[d].collect{|f|  url_for(f.sub(/\.\/investigation/,''),:full) if f.match(/\.txt$/) or f.match(/\d$/) }.compact.sort.join("\n") + "\n"
+      end
+
+      def dir
+        File.join File.dirname(File.expand_path __FILE__), "investigation", params[:id].to_s
+      end
+
+      def tmp
+        File.join dir,"tmp"
+      end
+
+      def file
+        File.join dir, params[:filename]
+      end
+
+      def n3
+        "#{params[:id]}.n3"
+      end
+
+      def next_id
+        id = Dir["./investigation/*"].collect{|f| File.basename(f).to_i}.sort.last
+        id ? id + 1 : 0
+      end
+
+      def prepare_upload
+        # lock tmp dir
+        locked_error "Processing investigation #{params[:id]}. Please try again later." if File.exists? tmp
+        bad_request_error "Please submit data as multipart/form-data" unless request.form_data?
+        # move existing ISA-TAB files to tmp
+        FileUtils.mkdir_p tmp
+        FileUtils.cp Dir[File.join(dir,"*.txt")], tmp
+        File.open(File.join(tmp, params[:file][:filename]), "w+"){|f| f.puts params[:file][:tempfile].read}
+      end
+
+      def extract_zip
+        # overwrite existing files with new submission
+        `unzip -o #{File.join(tmp,params[:file][:filename])} -d #{tmp}`
+        Dir["#{tmp}/*"].collect{|d| d if File.directory?(d)}.compact.each  do |d|
+          `mv #{d}/* #{tmp}`
+          `rmdir #{d}`
+        end
+      end
+
+      def extract_xls
+        # use Excelx.new instead of Excel.new if your file is a .xlsx
+        xls = Excel.new(File.join(tmp, params[:file][:filename])) if params[:file][:filename].match(/.xls$/)
+        xls = Excelx.new(File.join(tmp, params[:file][:filename])) if params[:file][:filename].match(/.xlsx$/)
+        xls.sheets.each_with_index do |sh, idx|
+          name = sh.to_s
+          xls.default_sheet = xls.sheets[idx]
+          1.upto(xls.last_row) do |ro|
+            1.upto(xls.last_column) do |co|
+              unless (co == xls.last_column)
+                File.open(File.join(tmp, name + ".txt"), "a+"){|f| f.print "#{xls.cell(ro, co)}\t"}
+              else
+                File.open(File.join(tmp, name + ".txt"), "a+"){|f| f.print "#{xls.cell(ro, co)}\n"}
+              end
+            end
+          end
+        end   
+      rescue
+        bad_request_error "Could not parse spreadsheet #{params[:file][:filename]}"
+      end
+
+      def isa2rdf
+        result = `cd #{File.dirname(__FILE__)}/java && java -jar isa2rdf-0.0.1-SNAPSHOT.jar -d #{tmp} -o #{File.join tmp,n3}` # warnings go to stdout, isa2rdf exits always with 0 
+        if result =~ /Invalid ISA-TAB/ or !File.exists? "#{File.join tmp,n3}" 
+          FileUtils.remove_entry tmp 
+          FileUtils.remove_entry dir
+          bad_request_error "ISA-TAB validation failed:\n"+result
+        end
+        # if everything is fine move ISA-TAB files back to original dir
+        FileUtils.cp Dir[File.join(tmp,"*")], dir
+        # git commit
+        newfiles = `cd #{File.dirname(__FILE__)}/investigation; git ls-files --others --exclude-standard --directory`
+        `cd #{File.dirname(__FILE__)}/investigation && git add #{newfiles}`
+        ['application/zip', 'application/vnd.ms-excel'].include?(params[:file][:type]) ? action = "created" : action = "modified"
+        `cd #{File.dirname(__FILE__)}/investigation && git commit -am "investigation #{params[:id]} #{action} by #{request.ip}"`
+        # create new zipfile
+        zipfile = File.join dir, "investigation_#{params[:id]}.zip"
+        `zip -j #{zipfile} #{dir}/*.txt`
+        # TODO: delete all RDF data for this investigation (partial updates and deletes)
+        # store RDF
+        length = File.size(File.join dir,n3)
+        file = File.join(dir,n3)
+        `curl -0 -u #{FOUR_STORE_USER}:#{FOUR_STORE_PASS} -T #{file} -H 'Content_Length => #{length}' '#{FOUR_STORE}/data/investigation#{n3}'`
+        FileUtils.remove_entry tmp  # unlocks tmp
+      end
+
+      def query
+        params.each{|k, v| @query = CGI.unescape(v)}
+        # use it like: "http://localhost/?query=SELECT * WHERE {?x ?p ?o}" in your browser
+        @result = `curl -i -u #{FOUR_STORE_USER}:#{FOUR_STORE_PASS} -d "query=#{@query}" '#{FOUR_STORE}/sparql/'`
+        @result.chomp    
+      end
+      
+      def query_all
+        @result = `curl -i -u #{FOUR_STORE_USER}:#{FOUR_STORE_PASS} -d "query=SELECT * WHERE {?x ?p ?o}" '#{FOUR_STORE}/sparql/'`
+        @result.chomp    
+      end
+    end
+
+    before do
+      not_found_error "Directory #{dir} does not exist."  unless File.exist? dir
+      @accept = request.env['HTTP_ACCEPT']
+      response['Content-Type'] = @accept
+      # TODO: A+A
+    end
+
+    # Query all investigations or get a list of all investigations
+    # Requests with a query parameter will perform a SPARQL query on all investigations
+    # @return [application/sparql-results+json] Query result
+    # @return [text/uri-list] List of investigations
+    get '/?' do
+      if params[:query] # "/?query=SELECT * WHERE {?s ?p ?o}"
+        # @param query SPARQL query
+        response['Content-type'] = "application/sparql-results+json"
+        query
+      elsif params[:query_all] # "/?query="
+        # Requests without a query string return a list of all sparql results (?s ?p ?o)
+        response['Content-type'] = "application/sparql-results+json"
+        query_all
+      else
+        # Requests without a query parameter return a list of all investigations
+        response['Content-Type'] = 'text/uri-list'
+        uri_list
+      end
+    end
+
+    # Create a new investigation from ISA-TAB files
+    # @param [Header] Content-type: multipart/form-data
+    # @param file Zipped investigation files in ISA-TAB format
+    # @return [text/uri-list] Investigation URI 
+    post '/?' do
+      params[:id] = next_id
+      mime_types = ['application/zip','text/tab-separated-values', "application/vnd.ms-excel"]
+      bad_request_error "Mime type #{params[:file][:type]} not supported. Please submit data as zip archive (application/zip), Excel file (application/vnd.ms-excel) or as tab separated text (text/tab-separated-values)" unless mime_types.include? params[:file][:type]
+      task = OpenTox::Task.create(TASK, :description => "#{params[:file][:filename]}: Uploding, validationg and converting to RDF") do
+        prepare_upload
+        case params[:file][:type]
+        when "application/vnd.ms-excel"
+          extract_xls
+        when "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+          extract_xls
+        when 'application/zip'
+          extract_zip
+        #when  'text/tab-separated-values' # do nothing, file is already in tmp
+        end
+        isa2rdf
+        uri
+      end
+      response['Content-Type'] = 'text/uri-list'
+      halt 202,task.uri+"\n"
+    end
+
+    # Get an investigation representation
+    # @param [Header] Accept: one of text/tab-separated-values, text/uri-list, application/zip, application/sparql-results+json
+    # @return [text/tab-separated-values, text/uri-list, application/zip, application/sparql-results+json] Investigation in the requested format
+    get '/:id' do
+      not_found_error "Investigation #{uri} does not exist."  unless File.exist? dir # not called in before filter???
+      case @accept
+      when "text/tab-separated-values"
+        send_file Dir["./investigation/#{params[:id]}/i_*txt"].first, :type => @accept
+      when "text/uri-list"
+        uri_list
+      when "application/zip"
+        send_file File.join dir, "investigation_#{params[:id]}.zip"
+      when "application/sparql-results+json"
+        query_all
+      else
+        #$logger.debug request.to_yaml
+        #bad_request_error "Accept header #{@accept} not supported for #{uri}"
+        $logger.warn "Accept header #{@accept} not supported for #{uri}" # do not halt: strange requests from test, TODO: identify and fix
+      end
+    end
+
+    # Add studies, assays or data to an investigation
+    # @param [Header] Content-type: multipart/form-data
+    # @param file Study, assay and data file (zip archive of ISA-TAB files or individual ISA-TAB files)
+    post '/:id' do
+      mime_types = ['application/zip','text/tab-separated-values', "application/vnd.ms-excel"]
+      bad_request_error "Mime type #{params[:file][:type]} not supported. Please submit data as zip archive (application/zip), Excel file (application/vnd.ms-excel) or as tab separated text (text/tab-separated-values)" unless mime_types.include? params[:file][:type]
+      task = OpenTox::Task.create(TASK, :description => "#{params[:file][:filename]}: Uploding, validationg and converting to RDF") do
+        prepare_upload
+        isa2rdf
+        uri
+      end
+      response['Content-Type'] = 'text/uri-list'
+      halt 202,task.uri+"\n"
+    end
+
+    # Delete an investigation
+    delete '/:id' do
+      FileUtils.remove_entry dir
+      # git commit
+      `cd #{File.dirname(__FILE__)}/investigation; git commit -am "#{dir} deleted by #{request.ip}"`
+      # updata RDF
+      `curl -i -u #{FOUR_STORE_USER}:#{FOUR_STORE_PASS} -X DELETE '#{FOUR_STORE}/data/investigation#{n3}'`
+      response['Content-Type'] = 'text/plain'
+      "investigation #{params[:id]} deleted"
+    end
+
+    # Get a study, assay, data representation
+    # @param [Header] one of text/tab-separated-values, application/sparql-results+json
+    # @return [text/tab-separated-values, application/sparql-results+json] Study, assay, data representation in ISA-TAB or RDF format
+    get '/:id/:filename'  do
+      case @accept
+      when "text/tab-separated-values"
+        send_file file, :type => @accept
+      when "application/sparql-results+json"
+        # TODO: return all data in rdf
+        not_implemented_error "SPARQL query not yet implemented"
+      else
+        bad_request_error "Accept header #{@accept} not supported"
+      end
+    end
+
+    # Delete an individual study, assay or data file
+    delete '/:id/:filename'  do
+      task = OpenTox::Task.create(TASK, :description => "Deleting #{params[:file][:filename]} from investigation #{params[:id]}.") do
+        prepare_upload
+        File.delete File.join(tmp,params[:filename])
+        isa2rdf
+        "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
+      end
+      response['Content-Type'] = 'text/uri-list'
+      halt 202,task.uri+"\n"
+    end
+
+  end
+end

data/bin/toxbank-investigation-install

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+#!/bin/sh
+# Main ToxBank-investigation install script
+# Author: Christoph Helma, Andreas Maunz, Denis Gebele.
+
+ISA2RDF=isa2rdf-0.0.1-SNAPSHOT.jar
+
+echo
+echo "This script will setup and configure the toxbank-investigation service."
+echo "You may have to run the script as root if the toxbank-invetigation gem has been installed as root (deprecated)"
+echo
+
+TB_HOME=`dirname $0`/..
+cd $TB_HOME
+TB_HOME=`pwd`
+mkdir -p investigation
+mkdir -p java
+mkdir -p public
+
+
+cd java
+if [ ! -f $ISA2RDF ]
+then
+  echo "Installing isa2rdf"
+  wget -v "https://github.com/downloads/ToxBank/isa2rdf/$ISA2RDF"
+fi
+cd $TB_HOME
+
+cd investigation
+if [ ! -d .git ]
+then
+  echo "Initializing git for investigations"
+  git init
+  echo "*/*.zip" > .gitignore
+  echo "*/tmp" >> .gitignore
+  git add .gitignore
+  git commit -am "Initial commit: .gitignore added"
+fi
+cd $TB_HOME
+
+echo "Installing configuration files"
+
+mkdir -p "$HOME/.opentox/config/toxbank-investigation" 
+mkdir -p "$HOME/.opentox/log" 
+mkdir -p "$HOME/.opentox/tmp" 
+
+config="$HOME/.opentox/config/toxbank-investigation/production.rb" 
+
+if [ -f $config ]
+then
+  echo "Configuration $config exists. Please check if the settings are correct."
+else
+  echo "Creating configuration"
+  echo "Please enter your 4store username:"
+  read user
+  echo "Please enter your 4store password:"
+  read pass
+
+  sed -e "s/\<USER\>/$user/;s/\<PASS\>/$pass/" config/production.rb > $config
+  echo "Configuration $config created. Please check if the settings are correct."
+fi
+
+echo
+echo "Installation finished and system configured."
+echo "Do you want to start the webserver? (y/n)"
+
+read answer
+if [ $answer = "y" ]
+then
+  last_ip=`ip addr show|grep -w inet|grep -v '127.0'|sed  's/ \+inet //'|cut -d '/' -f1|cut -d '.' -f4`
+  port=8`printf "%03d" $last_ip`
+  echo "Starting unicorn in production mode at port $port"
+  unicorn -p $port -E production -D 
+else
+  echo "Run 'unicorn -E production -D' to start the service. See 'unicorn -h' for more options"
+fi
+echo

data/config/production.rb

@@ -0,0 +1,9 @@
+TASK = "http://webservices.in-silico.ch/task"
+
+FOUR_STORE = "http://4store.in-silico.ch"
+FOUR_STORE_USER = GUEST
+FOUR_STORE_PASS = TOXBANK
+
+AA = "https://opensso.in-silico.ch"
+AA_USER = "guest"
+AA_PASS = "guest"

data/config.ru

@@ -0,0 +1,5 @@
+#require 'rubygems'
+require 'bundler'
+Bundler.require
+require './application.rb'
+run OpenTox::Application

data/java/config/isa_configurator/cellcount_flowcytometry.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="cellcount_flowcytometry" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="cell counting" term-accession="1111111" source-abbreviation="OBI"/><technology term-label="flow cytometry" term-accession="2222222" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the sample]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a name identifying the labeled sample.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a semi-colon separated value of dyes selected from CHEBI]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the assay]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Parameter Value[flow cytometry instrument]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[instrument]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[optical path]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the optical path]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[detector voltage]" data-type="Integer" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[detector voltage]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>unit"</description><recommended-ontologies><ontology id="1112" abbreviation="UO" name="Units of measurement" version="40305"/></recommended-ontologies></unit-field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[path to image file]]></description><default-value><![CDATA[]]></default-value></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[path to fcs datafile]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="gating"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a data transformation carried out on the raw data files]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[path to gating-ml file]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/cellsorting_flowcyt.xml

@@ -0,0 +1,5 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="cellsorting_flowcyt" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="cell sorting" term-accession="" source-abbreviation=""/><technology term-label="flow cytometry" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the sample]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
+            </generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a labeled sample name]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
+            </generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a semi-colon separated value of dyes selected from CHEBI]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the assay]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
+                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]
+            </generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Parameter Value[flow cytometry instrument]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the name of the flow cytometer used]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[optical path]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the optical path]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[detector voltage]" data-type="Integer" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a voltage value]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>voltage"</description><recommended-ontologies><ontology id="1112" abbreviation="UO" name="Units of measurement" version="40305"/></recommended-ontologies></unit-field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a path to an image file]]></description><default-value><![CDATA[]]></default-value></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[fcs files]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="gating"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the name identifying the sample]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a derived data file (e.g gating.ml file)]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/clinical_chemistry.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="clinical_chemistry" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="clinical chemistry analysis" term-accession="" source-abbreviation="OBI"/><technology term-label="" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="clinical chemistry"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied.]]></description><default-value><![CDATA[]]></default-value></field><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/copynumvariation_micro.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="copynumvariation_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="copy number variation profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="DNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/dnamethylation_micro.xml

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+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="dnamethylation_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="DNA methylation profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="DNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[derived array data matrix]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/dnamethylation_seq.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="dnamethylation_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="DNA methylation profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Parameter Value[cross linking]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a protocol parameter specific to Chromatin immuprecipitation in this context]]></description><default-value><![CDATA[]]></default-value><list-values>uv-light,formaldehyde,di-tert-butyl peroxide,formaldehyde and di-tert-butyl peroxyde</list-values></field><field header="Parameter Value[DNA fragmentation]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter value to report the method used for shearing DNA. Classic methods are sonication, nebulisation]]></description><default-value><![CDATA[]]></default-value><list-values>sonication,nebulization,micrococcal nuclease digestion,deoxyribonuclease digestion</list-values></field><field header="Parameter Value[DNA fragment size]" data-type="Double" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the intended DNA fragment size resulting from the DNA fragmentation process (aka DNA shearing)]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>unit to express nucleic acid size"</description></unit-field><field header="Parameter Value[immunoprecipitation antibody]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report immunoprecipitation antibody details. Structure information as follows: antibody name;antibody manufacturer;antibody catalog number;antibody dilution factor;clonality]]></description><default-value><![CDATA[]]></default-value></field><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library strategy]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Sequencing technique intended for this library (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>Bisulfite-Seq,MRE-Seq,MeDIP-Seq,MBD-Seq,OTHER</list-values></field><field header="Parameter Value[library selection]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>PCR,RANDOM-PCR,HMPR,MF,MSLL,5-methylcytidine antibody,MBD2 protein methyl-CpG binding domain,other,unspecified</list-values></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool. The field can be repeated in case more than one barcode is used when building a library]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/envgen_survey_seq.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="envgen_survey_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="environmental gene survey" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[target_taxon]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[provide the taxonomic group targeted by this survey. for instance Archae, Bacteria, Eukaryota]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[target_gene]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, report the gene of interest used to monitor diversity]]></description><default-value><![CDATA[]]></default-value><list-values>16S rRNA,18S rRNA,nif,amoA,rpo</list-values></field><field header="Parameter Value[target_subfragment]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, depends on declaring a target_gene, allows added specificity]]></description><default-value><![CDATA[]]></default-value><list-values>V6,V9,ITS</list-values></field><field header="Parameter Value[pcr_primers]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[pcr_cond]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/genome_seq.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="genome_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="genome sequencing" term-accession="" source-abbreviation=""/><technology term-label="nucleotide sequencing" term-accession="e.g. 12345" source-abbreviation="e.g. OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[sample name]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library source]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)]]></description><default-value><![CDATA[GENOMIC]]></default-value></field><field header="Parameter Value[library strategy]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Sequencing technique intended for this library (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>AMPLICON,OTHER</list-values></field><field header="Parameter Value[library selection]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[quality scorer]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[ENA term if applicable]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[base caller]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[ENA term if applicable]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[assayname]]></description><default-value><![CDATA[]]></default-value></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[raw data]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence assembly"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a data transformation]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[derived data such as an assembly file]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/hematology.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="hematology" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="hematology" term-accession="" source-abbreviation="OBI"/><technology term-label="" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="hematology"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied.]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/heterozygosity_micro.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="heterozygosity_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="loss of heterozygosity profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="DNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/histology.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="histology" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="histology" term-accession="" source-abbreviation="OBI"/><technology term-label="" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="histology"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/histonemodification_seq.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="histonemodification_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="histone modification profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Parameter Value[cross linking]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a protocol parameter specific to chromatin immuprecipitation in this context]]></description><default-value><![CDATA[]]></default-value><list-values>uv-light,formaldehyde,di-tert-butyl peroxide,formaldehyde and di-tert-butyl peroxyde</list-values></field><field header="Parameter Value[DNA fragmentation]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter value to report the method used for shearing DNA. Classic methods are sonication, nebulisation]]></description><default-value><![CDATA[]]></default-value><list-values>sonication,nebulization,micrococcal nuclease digestion,deoxyribonuclease digestion</list-values></field><field header="Parameter Value[DNA fragment size]" data-type="Double" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the intended DNA fragment size resulting from the DNA fragmentation process (aka DNA shearing)]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>unit to express nucleic acid size"</description></unit-field><field header="Parameter Value[immunoprecipitation antibody]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report immunoprecipitation antibody details. Structure information as follows: antibody name;antibody manufacturer;antibody catalog number;antibody dilution factor;clonality]]></description><default-value><![CDATA[]]></default-value></field><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>