toxbank-investigation 0.0.1pre-x86-linux

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  1. data/.gitignore +11 -0
  2. data/Gemfile +7 -0
  3. data/Gemfile.lock +101 -0
  4. data/LICENSE +674 -0
  5. data/README +14 -0
  6. data/Rakefile +31 -0
  7. data/application.rb +246 -0
  8. data/bin/toxbank-investigation-install +76 -0
  9. data/config/production.rb +9 -0
  10. data/config.ru +5 -0
  11. data/java/config/isa_configurator/cellcount_flowcytometry.xml +1 -0
  12. data/java/config/isa_configurator/cellsorting_flowcyt.xml +5 -0
  13. data/java/config/isa_configurator/clinical_chemistry.xml +1 -0
  14. data/java/config/isa_configurator/copynumvariation_micro.xml +1 -0
  15. data/java/config/isa_configurator/dnamethylation_micro.xml +1 -0
  16. data/java/config/isa_configurator/dnamethylation_seq.xml +1 -0
  17. data/java/config/isa_configurator/envgen_survey_seq.xml +1 -0
  18. data/java/config/isa_configurator/genome_seq.xml +1 -0
  19. data/java/config/isa_configurator/hematology.xml +1 -0
  20. data/java/config/isa_configurator/heterozygosity_micro.xml +1 -0
  21. data/java/config/isa_configurator/histology.xml +1 -0
  22. data/java/config/isa_configurator/histonemodification_seq.xml +1 -0
  23. data/java/config/isa_configurator/metaboliteprofiling_ms.xml +114 -0
  24. data/java/config/isa_configurator/metaboliteprofiling_nmr.xml +114 -0
  25. data/java/config/isa_configurator/metagenome_seq.xml +1 -0
  26. data/java/config/isa_configurator/nru_assay.xml +8 -0
  27. data/java/config/isa_configurator/ppi_detection_micro.xml +1 -0
  28. data/java/config/isa_configurator/protein_dna_binding_ident_micro.xml +1 -0
  29. data/java/config/isa_configurator/protein_dna_binding_ident_seq.xml +1 -0
  30. data/java/config/isa_configurator/protein_expression_ge.xml +101 -0
  31. data/java/config/isa_configurator/protein_expression_micro.xml +1 -0
  32. data/java/config/isa_configurator/protein_expression_ms.xml +1 -0
  33. data/java/config/isa_configurator/proteinident_ms.xml +1 -0
  34. data/java/config/isa_configurator/snpanalysis_micro.xml +1 -0
  35. data/java/config/isa_configurator/studySample.xml +1 -0
  36. data/java/config/isa_configurator/tfbsident_micro.xml +1 -0
  37. data/java/config/isa_configurator/tfbsident_seq.xml +1 -0
  38. data/java/config/isa_configurator/transcription_micro.xml +1 -0
  39. data/java/config/isa_configurator/transcription_rtpcr.xml +1 -0
  40. data/java/config/isa_configurator/transcription_seq.xml +6 -0
  41. data/test/Rakefile +48 -0
  42. data/test/all.rb +3 -0
  43. data/test/authorization.rb +112 -0
  44. data/test/basic_rest.rb +98 -0
  45. data/test/data/invalid/BII-invalid.n3 +19641 -0
  46. data/test/data/invalid/a_TB-ACCUTOX-plate1.txt +97 -0
  47. data/test/data/invalid/a_TB-ACCUTOX-plate2.txt +97 -0
  48. data/test/data/invalid/a_TB-ACCUTOX-plate3.txt +97 -0
  49. data/test/data/invalid/acetaminophen-plate1-data.txt +97 -0
  50. data/test/data/invalid/acetaminophen-plate2-data.txt +97 -0
  51. data/test/data/invalid/acetaminophen-plate3-data.txt +97 -0
  52. data/test/data/invalid/i_Investigation.txt +156 -0
  53. data/test/data/invalid/ic50.txt +20 -0
  54. data/test/data/invalid/isa_TB_ACCUTOX.xls +0 -0
  55. data/test/data/invalid/isa_TB_ACCUTOX.zip +0 -0
  56. data/test/data/invalid/s_TB-ACCUTOX-acetaminophen.txt +58 -0
  57. data/test/data/valid/BII-I-1.n3 +19648 -0
  58. data/test/data/valid/BII-I-1.rdf +19648 -0
  59. data/test/data/valid/BII-I-1.zip +0 -0
  60. data/test/data/valid/isa-tab-renamed.zip +0 -0
  61. data/test/data/valid/isa_TB_BII.xls +0 -0
  62. data/test/httpd.rb +69 -0
  63. data/test/querytest.rb +42 -0
  64. data/test/upload.rb +152 -0
  65. data/test/xls_upload.rb +60 -0
  66. data/toxbank-investigation.gemspec +29 -0
  67. metadata +133 -0
data/java/config/isa_configurator/metaboliteprofiling_ms.xml ADDED
@@ -0,0 +1,114 @@
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
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+ <isatab-configuration table-name="metaboliteprofiling_ms" isatab-assay-type="ms_spec_assay"
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+ isatab-conversion-target="generic">
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+ <measurement term-label="metabolite profiling" term-accession="0000366" source-abbreviation="OBI"/>
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+ <technology term-label="mass spectrometry" term-accession="" source-abbreviation="OBI"/>
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+ <field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true"
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+ is-hidden="false">
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+ <description>
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+ <![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
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+ </generated-value-template>
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+ </field>
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+ <protocol-field protocol-type="extraction"/>
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+ <field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="true" is-hidden="false">
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+ <description><![CDATA[User-defined names for each portion of extracted material.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>
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+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
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+ </generated-value-template>
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+ </field>
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+ <protocol-field protocol-type="labeling"/>
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+ <field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[Identifier for the labeled extract.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>
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+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]
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+ </generated-value-template>
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+ </field>
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+ <field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![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>
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+ <default-value><![CDATA[]]></default-value>
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+ <recommended-ontologies>
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+ <ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest"
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+ version="40664"/>
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+ </recommended-ontologies>
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+ </field>
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+ <protocol-field protocol-type="mass spectrometry"/>
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+ <field header="Parameter Value[instrument]" data-type="Ontology term" is-file-field="false"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description><![CDATA[the name of the mass spectrometry instrument]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <recommended-ontologies>
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+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
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+ </recommended-ontologies>
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+ </field>
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+ <field header="Parameter Value[ion source]" data-type="Ontology term" is-file-field="false"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description><![CDATA[the ion source used by the mass spectrometer, use PSI-MS cv]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <recommended-ontologies>
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+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
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+ </recommended-ontologies>
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+ </field>
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+ <field header="Parameter Value[detector]" data-type="Ontology term" is-file-field="false"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description><![CDATA[the detector used by the mass spectrometer, use PSI-MS cv]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <recommended-ontologies>
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+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
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+ </recommended-ontologies>
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+ </field>
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+ <field header="Parameter Value[analyzer]" data-type="Ontology term" is-file-field="false"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description><![CDATA[the analyzer(s) used by the mass spectrometer, use PSI-MS cv]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <recommended-ontologies>
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+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
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+ </recommended-ontologies>
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+ </field>
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+ <field header="MS Assay Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="true" is-hidden="false">
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+ <description><![CDATA[User-defined name for a MS assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>
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+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].MSASSAY-[HYB_COUNT]
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+ </generated-value-template>
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+ </field>
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+ <field header="Raw Spectral Data File" data-type="String" is-file-field="true" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[Name (or URI) of the raw spectral data file generated by an assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <protocol-field protocol-type="data transformation"/>
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+ <field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[User-defined name for each normalization applied]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[User-defined name for each data transformation applied]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Derived Spectral Data File" data-type="String" is-file-field="true" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[Name (or URI) of the derived data file generated from spectral data by an assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <protocol-field protocol-type="identification"/>
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+ <field header="Metabolite Assignment File" data-type="String" is-file-field="true" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[Name (or URI) of the metabolite assignment file gathered for this assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <structured-field name="Factors"/>
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+ </isatab-configuration>
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+ </isatab-config-file>
data/java/config/isa_configurator/metaboliteprofiling_nmr.xml ADDED
@@ -0,0 +1,114 @@
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
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+ <isatab-configuration table-name="metaboliteprofiling_nmr" isatab-assay-type="nmr_spec_assay"
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+ isatab-conversion-target="generic">
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+ <measurement term-label="metabolite profiling" term-accession="0000366" source-abbreviation="OBI"/>
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+ <technology term-label="NMR spectroscopy" term-accession="" source-abbreviation="OBI"/>
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+ <field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true"
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+ is-hidden="false">
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+ <description>
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+ <![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
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+ </generated-value-template>
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+ </field>
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+ <protocol-field protocol-type="extraction"/>
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+ <field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[User-defined names for each portion of extracted material.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>
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+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
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+ </generated-value-template>
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+ </field>
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+ <protocol-field protocol-type="labeling"/>
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+ <field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[Identifier for the labeled extract.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>
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+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]
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+ </generated-value-template>
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+ </field>
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+ <field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![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>
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+ <default-value><![CDATA[]]></default-value>
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+ <recommended-ontologies>
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+ <ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest"
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+ version="40664"/>
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+ </recommended-ontologies>
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+ </field>
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+ <protocol-field protocol-type="NMR spectroscopy"/>
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+ <field header="Parameter Value[instrument]" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[the name of the NMR instrument]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Parameter Value[NMR Probe]" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[the type of probe fitted to the spectroscope]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Parameter Value[number of acquisition]" data-type="String" is-file-field="false"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[a parameter to indicate the number of acquisition used to generate the fid]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Parameter Value[magnetic field strength]" data-type="String" is-file-field="false"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description><![CDATA[a parameter expressed in tesla to report the strength of the]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <unit-field data-type="Ontology term" is-multiple-value="false" is-required="true">
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+ <description>unit"</description>
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+ </unit-field>
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+ <field header="Acquisition Parameter Data File" data-type="String" is-file-field="true"
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+ is-multiple-value="false" is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[Name (or URI) of the acquisition parameter data file gathered for this assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <protocol-field protocol-type="nmr assay"/>
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+ <field header="NMR Assay Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="true" is-hidden="false">
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+ <description><![CDATA[User-defined name for a NMR assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ <generated-value-template>
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+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].NMRASSAY-[HYB_COUNT]
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+ </generated-value-template>
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+ </field>
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+ <field header="Free Induction Decay Data File" data-type="String" is-file-field="true" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[Name (or URI) of the free induction decay data file gathered for this assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <protocol-field protocol-type="data normalization"/>
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+ <field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[User-defined name for each normalization applied]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <protocol-field protocol-type="data transformation"/>
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+ <field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true"
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+ is-required="false" is-hidden="false">
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+ <description><![CDATA[User-defined name for each data transformation applied]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Derived Spectral Data File" data-type="String" is-file-field="true" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[Name (or URI) of the derived data file generated from spectral data by an assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <field header="Metabolite Assignment File" data-type="String" is-file-field="true" is-multiple-value="false"
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+ is-required="false" is-hidden="false">
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+ <description>
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+ <![CDATA[Name (or URI) of the metabolite assignment file gathered for this assay.]]></description>
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+ <default-value><![CDATA[]]></default-value>
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+ </field>
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+ <structured-field name="Factors"/>
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+ </isatab-configuration>
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+ </isatab-config-file>
data/java/config/isa_configurator/metagenome_seq.xml ADDED
@@ -0,0 +1 @@
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="metagenome_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="metagenome sequencing" 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="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 ="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[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="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,Restriction Digest,size fractionation,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.]]></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="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 Data 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 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/nru_assay.xml ADDED
@@ -0,0 +1,8 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="nru_assay" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="Cell viability" term-accession="0000090" source-abbreviation="BAO"/><technology term-label="Neutral Red Uptake Cytotoxicity Test" 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[Should be linked to NRU template Sample Name field]]></description><default-value><![CDATA[
2
+
3
+ ]]></default-value></field><field header="Characteristics[well]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Well in a 96 well plate]]></description><default-value><![CDATA[
4
+ A1
5
+ ]]></default-value></field>
6
+ <protocol-field protocol-type ="Neutral Red Uptake (NRU) Cytotoxicity Test"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier of the well ?]]></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="true" is-hidden="false"><description><![CDATA[Data file]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="dose response curve"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Dose response derived data]]></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[IC50]]></description><default-value><![CDATA[]]></default-value></field>
7
+ <structured-field name="Factors"/>
8
+ </isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/ppi_detection_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="ppi_detection_micro" isatab-assay-type="generic_assay" isatab-conversion-target="magetab"><measurement term-label="protein-protein interaction detection" term-accession="0000288" source-abbreviation="OBI"/><technology term-label="protein microarray" term-accession="0400149" 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 ="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 ="protocol"/><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 ="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><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 normalization"/><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[derived data file]]></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="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/protein_dna_binding_ident_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="protein_dna_binding_ident_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="protein-DNA binding site identification" term-accession="" source-abbreviation=""/><technology term-label="DNA microarray" 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 preparation"/><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 ="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="true" 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/protein_dna_binding_ident_seq.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="protein_dna_binding_ident_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="protein-DNA binding site identification" term-accession="" source-abbreviation=""/><technology term-label="nucleotide sequencing" term-accession="" 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 ="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.]]></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[quality score]" 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="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 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/protein_expression_ge.xml ADDED
@@ -0,0 +1,101 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
2
+ <isatab-configuration table-name="protein_expression_ge" isatab-assay-type="gel_electrophoresis_assay"
3
+ isatab-conversion-target="generic">
4
+ <measurement term-label="protein expression profiling" term-accession="" source-abbreviation="OBI"/>
5
+ <technology term-label="gel electrophoresis" term-accession="" source-abbreviation="OBI"/>
6
+ <field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true"
7
+ is-hidden="false">
8
+ <description>
9
+ <![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description>
10
+ <default-value><![CDATA[]]></default-value>
11
+ <generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
12
+ </generated-value-template>
13
+ </field>
14
+ <protocol-field protocol-type="protein extraction"/>
15
+ <field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
16
+ is-required="true" is-hidden="false">
17
+ <description><![CDATA[User-defined names for each portion of extracted material.]]></description>
18
+ <default-value><![CDATA[]]></default-value>
19
+ <generated-value-template>
20
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
21
+ </generated-value-template>
22
+ </field>
23
+ <protocol-field protocol-type="labeling"/>
24
+ <field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
25
+ is-required="false" is-hidden="false">
26
+ <description><![CDATA[Identifier for the labeled extract.]]></description>
27
+ <default-value><![CDATA[]]></default-value>
28
+ <generated-value-template>
29
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]
30
+ </generated-value-template>
31
+ </field>
32
+ <field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false"
33
+ is-required="false" is-hidden="false">
34
+ <description>
35
+ <![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>
36
+ <default-value><![CDATA[]]></default-value>
37
+ <recommended-ontologies>
38
+ <ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest"
39
+ version="40664"/>
40
+ </recommended-ontologies>
41
+ </field>
42
+ <protocol-field protocol-type="electrophoresis"/>
43
+ <field header="Gel Electrophoresis Assay Name" data-type="String" is-file-field="false"
44
+ is-multiple-value="false" is-required="true" is-hidden="false">
45
+ <description><![CDATA[User-defined name for a gel electrophoresis assay.]]></description>
46
+ <default-value><![CDATA[]]></default-value>
47
+ <generated-value-template>
48
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].GEASSAY-[HYB_COUNT]
49
+ </generated-value-template>
50
+ </field>
51
+ <field header="First Dimension" data-type="Ontology term" is-file-field="false" is-multiple-value="false"
52
+ is-required="true" is-hidden="false">
53
+ <description><![CDATA[First dimension of the 2d gel]]></description>
54
+ <default-value><![CDATA[]]></default-value>
55
+ </field>
56
+ <field header="Second Dimension" data-type="Ontology term" is-file-field="false" is-multiple-value="false"
57
+ is-required="true" is-hidden="false">
58
+ <description><![CDATA[Second dimension of the 2d gel.]]></description>
59
+ <default-value><![CDATA[]]></default-value>
60
+ </field>
61
+ <protocol-field protocol-type="data collection"/>
62
+ <field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false"
63
+ is-hidden="false">
64
+ <description><![CDATA[User-defined name for each scan event.]]></description>
65
+ <default-value><![CDATA[]]></default-value>
66
+ </field>
67
+ <field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false"
68
+ is-hidden="false">
69
+ <description><![CDATA[Name (or URI) of the image files generated by an assay]]></description>
70
+ <default-value><![CDATA[]]></default-value>
71
+ </field>
72
+ <field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false"
73
+ is-required="true" is-hidden="false">
74
+ <description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description>
75
+ <default-value><![CDATA[]]></default-value>
76
+ </field>
77
+ <protocol-field protocol-type="normalization"/>
78
+ <field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false"
79
+ is-required="false" is-hidden="false">
80
+ <description><![CDATA[User-defined name for each normalization applied]]></description>
81
+ <default-value><![CDATA[]]></default-value>
82
+ </field>
83
+ <protocol-field protocol-type="data transformation"/>
84
+ <field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false"
85
+ is-required="false" is-hidden="false">
86
+ <description><![CDATA[User-defined name for each data transformation applied]]></description>
87
+ <default-value><![CDATA[]]></default-value>
88
+ </field>
89
+ <field header="Spot Picking File" data-type="String" is-file-field="true" is-multiple-value="false"
90
+ is-required="false" is-hidden="false">
91
+ <description><![CDATA[Name (or URI) of the spot picking file used for this assay.]]></description>
92
+ <default-value><![CDATA[]]></default-value>
93
+ </field>
94
+ <field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false"
95
+ is-required="false" is-hidden="false">
96
+ <description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description>
97
+ <default-value><![CDATA[]]></default-value>
98
+ </field>
99
+ <structured-field name="Factors"/>
100
+ </isatab-configuration>
101
+ </isatab-config-file>
data/java/config/isa_configurator/protein_expression_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="protein_expression_micro" isatab-assay-type="generic_assay" isatab-conversion-target="magetab"><measurement term-label="protein expression profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="protein microarray" term-accession="0400149" 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 ="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 ="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="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="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><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/protein_expression_ms.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="protein_expression_ms" isatab-assay-type="ms_spec_assay" isatab-conversion-target="prideml"><measurement term-label="protein expression profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="mass spectrometry" 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 ="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="false" 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="false" 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 ="mass spectrometry"/><field header="Parameter Value[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 mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="Parameter Value[ion source]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the ion source used by the mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="Parameter Value[detector]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the detector used by the mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="Parameter Value[analyzer]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the analyzer used by the mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="MS 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 a MS 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].MSASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Spectral 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 raw spectral data file generated by an assay.]]></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="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Spectral 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 derived data file generated from spectral data by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="identification"/><field header="Peptide Assignment 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 peptide assignment file gathered for this assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Protein Assignment 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 protein assignment file gathered for this assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Post Translational Modification Assignment 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 post translational modification file gathered for this assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/proteinident_ms.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="proteinident_ms" isatab-assay-type="ms_spec_assay" isatab-conversion-target="prideml"><measurement term-label="protein identification" term-accession="" source-abbreviation="OBI"/><technology term-label="mass spectrometry" 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 ="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="false" 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="false" 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 ="mass spectrometry"/><field header="Parameter Value[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 mass spectrometer. term from PSI-MS]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="Parameter Value[ion source]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the ion source used by the mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="Parameter Value[detector]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the detector used by the mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="Parameter Value[analyzer]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the analyzer or analyzers used by the mass spectrometer, use PSI-MS cv]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/></recommended-ontologies></field><field header="MS 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 a MS 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].MSASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Spectral 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 raw spectral data file generated by an assay.]]></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="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Spectral Data File" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the derived data file generated from spectral data by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="identification"/><field header="Peptide Assignment 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 peptide assignment file gathered for this assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Protein Assignment 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 protein assignment file gathered for this assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Post Translational Modification Assignment 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 post translational modification assignment file gathered for this assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/snpanalysis_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="snpanalysis_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="SNP analysis" term-accession="0000435" 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="true" 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/studySample.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="studySample"><measurement term-label="[Sample]" term-accession="e.g. 12345" source-abbreviation="e.g. OBI"/><technology term-label="" term-accession="e.g. 12345" source-abbreviation="e.g. OBI"/><field header="Source Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Sources are considered as the starting biological material used in a study.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO]</generated-value-template></field><field header="Characteristics[organism]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Provide a taxonomic information associated to the Source Biological material (for example, Species, genus, strain,....). Ideally, provide NCBI TaxID or NEWT identifier]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sample collection"/><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><structured-field name="Characteristics"/><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/tfbsident_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="tfbsident_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="transcription factor binding site identification" term-accession="0000291" 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 ="chromatin immunoprecipitation assays"/><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="true" 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="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/tfbsident_seq.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="tfbsident_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="transcription factor binding site identification" term-accession="0000291" 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[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="true" 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><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 score]" 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 scorer 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="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 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>