toxbank-investigation 0.0.2pre

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  1. data/.gitignore +11 -0
  2. data/Gemfile +12 -0
  3. data/Gemfile.lock +111 -0
  4. data/LICENSE +674 -0
  5. data/README +34 -0
  6. data/Rakefile +14 -0
  7. data/application.rb +284 -0
  8. data/bin/toxbank-investigation-install +76 -0
  9. data/config.ru +6 -0
  10. data/config/production.rb +9 -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/toxbank-investigation.gemspec +29 -0
  42. metadata +108 -0
data/java/config/isa_configurator/dnamethylation_micro.xml ADDED
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="dnamethylation_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="DNA methylation profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="DNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[derived array data matrix]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/dnamethylation_seq.xml ADDED
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="dnamethylation_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="DNA methylation profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Parameter Value[cross linking]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a protocol parameter specific to Chromatin immuprecipitation in this context]]></description><default-value><![CDATA[]]></default-value><list-values>uv-light,formaldehyde,di-tert-butyl peroxide,formaldehyde and di-tert-butyl peroxyde</list-values></field><field header="Parameter Value[DNA fragmentation]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter value to report the method used for shearing DNA. Classic methods are sonication, nebulisation]]></description><default-value><![CDATA[]]></default-value><list-values>sonication,nebulization,micrococcal nuclease digestion,deoxyribonuclease digestion</list-values></field><field header="Parameter Value[DNA fragment size]" data-type="Double" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the intended DNA fragment size resulting from the DNA fragmentation process (aka DNA shearing)]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>unit to express nucleic acid size"</description></unit-field><field header="Parameter Value[immunoprecipitation antibody]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report immunoprecipitation antibody details. Structure information as follows: antibody name;antibody manufacturer;antibody catalog number;antibody dilution factor;clonality]]></description><default-value><![CDATA[]]></default-value></field><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library strategy]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Sequencing technique intended for this library (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>Bisulfite-Seq,MRE-Seq,MeDIP-Seq,MBD-Seq,OTHER</list-values></field><field header="Parameter Value[library selection]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>PCR,RANDOM-PCR,HMPR,MF,MSLL,5-methylcytidine antibody,MBD2 protein methyl-CpG binding domain,other,unspecified</list-values></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool. The field can be repeated in case more than one barcode is used when building a library]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/envgen_survey_seq.xml ADDED
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="envgen_survey_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="environmental gene survey" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[target_taxon]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[provide the taxonomic group targeted by this survey. for instance Archae, Bacteria, Eukaryota]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[target_gene]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, report the gene of interest used to monitor diversity]]></description><default-value><![CDATA[]]></default-value><list-values>16S rRNA,18S rRNA,nif,amoA,rpo</list-values></field><field header="Parameter Value[target_subfragment]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, depends on declaring a target_gene, allows added specificity]]></description><default-value><![CDATA[]]></default-value><list-values>V6,V9,ITS</list-values></field><field header="Parameter Value[pcr_primers]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[pcr_cond]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/genome_seq.xml ADDED
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+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="genome_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="genome sequencing" term-accession="" source-abbreviation=""/><technology term-label="nucleotide sequencing" term-accession="e.g. 12345" source-abbreviation="e.g. OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[sample name]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library source]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)]]></description><default-value><![CDATA[GENOMIC]]></default-value></field><field header="Parameter Value[library strategy]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Sequencing technique intended for this library (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>AMPLICON,OTHER</list-values></field><field header="Parameter Value[library selection]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[quality scorer]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[ENA term if applicable]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[base caller]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[ENA term if applicable]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[assayname]]></description><default-value><![CDATA[]]></default-value></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[raw data]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence assembly"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a data transformation]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[derived data such as an assembly file]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/hematology.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="hematology" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="hematology" term-accession="" source-abbreviation="OBI"/><technology term-label="" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="hematology"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied.]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/heterozygosity_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="heterozygosity_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="loss of heterozygosity profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="DNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/histology.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="histology" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="histology" term-accession="" source-abbreviation="OBI"/><technology term-label="" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="histology"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/histonemodification_seq.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="histonemodification_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="histone modification profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Parameter Value[cross linking]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a protocol parameter specific to chromatin immuprecipitation in this context]]></description><default-value><![CDATA[]]></default-value><list-values>uv-light,formaldehyde,di-tert-butyl peroxide,formaldehyde and di-tert-butyl peroxyde</list-values></field><field header="Parameter Value[DNA fragmentation]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter value to report the method used for shearing DNA. Classic methods are sonication, nebulisation]]></description><default-value><![CDATA[]]></default-value><list-values>sonication,nebulization,micrococcal nuclease digestion,deoxyribonuclease digestion</list-values></field><field header="Parameter Value[DNA fragment size]" data-type="Double" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the intended DNA fragment size resulting from the DNA fragmentation process (aka DNA shearing)]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>unit to express nucleic acid size"</description></unit-field><field header="Parameter Value[immunoprecipitation antibody]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report immunoprecipitation antibody details. Structure information as follows: antibody name;antibody manufacturer;antibody catalog number;antibody dilution factor;clonality]]></description><default-value><![CDATA[]]></default-value></field><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/metaboliteprofiling_ms.xml ADDED
@@ -0,0 +1,114 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
2
+ <isatab-configuration table-name="metaboliteprofiling_ms" isatab-assay-type="ms_spec_assay"
3
+ isatab-conversion-target="generic">
4
+ <measurement term-label="metabolite profiling" term-accession="0000366" source-abbreviation="OBI"/>
5
+ <technology term-label="mass spectrometry" 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="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="mass spectrometry"/>
43
+ <field header="Parameter Value[instrument]" data-type="Ontology term" is-file-field="false"
44
+ is-multiple-value="false" is-required="false" is-hidden="false">
45
+ <description><![CDATA[the name of the mass spectrometry instrument]]></description>
46
+ <default-value><![CDATA[]]></default-value>
47
+ <recommended-ontologies>
48
+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
49
+ </recommended-ontologies>
50
+ </field>
51
+ <field header="Parameter Value[ion source]" data-type="Ontology term" is-file-field="false"
52
+ is-multiple-value="false" is-required="false" is-hidden="false">
53
+ <description><![CDATA[the ion source used by the mass spectrometer, use PSI-MS cv]]></description>
54
+ <default-value><![CDATA[]]></default-value>
55
+ <recommended-ontologies>
56
+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
57
+ </recommended-ontologies>
58
+ </field>
59
+ <field header="Parameter Value[detector]" data-type="Ontology term" is-file-field="false"
60
+ is-multiple-value="false" is-required="false" is-hidden="false">
61
+ <description><![CDATA[the detector used by the mass spectrometer, use PSI-MS cv]]></description>
62
+ <default-value><![CDATA[]]></default-value>
63
+ <recommended-ontologies>
64
+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
65
+ </recommended-ontologies>
66
+ </field>
67
+ <field header="Parameter Value[analyzer]" data-type="Ontology term" is-file-field="false"
68
+ is-multiple-value="false" is-required="false" is-hidden="false">
69
+ <description><![CDATA[the analyzer(s) used by the mass spectrometer, use PSI-MS cv]]></description>
70
+ <default-value><![CDATA[]]></default-value>
71
+ <recommended-ontologies>
72
+ <ontology id="1105" abbreviation="MS" name="Mass spectrometry" version="40763"/>
73
+ </recommended-ontologies>
74
+ </field>
75
+ <field header="MS Assay Name" data-type="String" is-file-field="false" is-multiple-value="false"
76
+ is-required="true" is-hidden="false">
77
+ <description><![CDATA[User-defined name for a MS assay.]]></description>
78
+ <default-value><![CDATA[]]></default-value>
79
+ <generated-value-template>
80
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].MSASSAY-[HYB_COUNT]
81
+ </generated-value-template>
82
+ </field>
83
+ <field header="Raw Spectral Data File" data-type="String" is-file-field="true" is-multiple-value="false"
84
+ is-required="false" is-hidden="false">
85
+ <description><![CDATA[Name (or URI) of the raw spectral data file generated by an assay.]]></description>
86
+ <default-value><![CDATA[]]></default-value>
87
+ </field>
88
+ <protocol-field protocol-type="data transformation"/>
89
+ <field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false"
90
+ is-required="false" is-hidden="false">
91
+ <description><![CDATA[User-defined name for each normalization applied]]></description>
92
+ <default-value><![CDATA[]]></default-value>
93
+ </field>
94
+ <field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true"
95
+ is-required="false" is-hidden="false">
96
+ <description><![CDATA[User-defined name for each data transformation applied]]></description>
97
+ <default-value><![CDATA[]]></default-value>
98
+ </field>
99
+ <field header="Derived Spectral Data File" data-type="String" is-file-field="true" is-multiple-value="false"
100
+ is-required="false" is-hidden="false">
101
+ <description>
102
+ <![CDATA[Name (or URI) of the derived data file generated from spectral data by an assay.]]></description>
103
+ <default-value><![CDATA[]]></default-value>
104
+ </field>
105
+ <protocol-field protocol-type="identification"/>
106
+ <field header="Metabolite Assignment File" data-type="String" is-file-field="true" is-multiple-value="false"
107
+ is-required="false" is-hidden="false">
108
+ <description>
109
+ <![CDATA[Name (or URI) of the metabolite assignment file gathered for this assay.]]></description>
110
+ <default-value><![CDATA[]]></default-value>
111
+ </field>
112
+ <structured-field name="Factors"/>
113
+ </isatab-configuration>
114
+ </isatab-config-file>
data/java/config/isa_configurator/metaboliteprofiling_nmr.xml ADDED
@@ -0,0 +1,114 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
2
+ <isatab-configuration table-name="metaboliteprofiling_nmr" isatab-assay-type="nmr_spec_assay"
3
+ isatab-conversion-target="generic">
4
+ <measurement term-label="metabolite profiling" term-accession="0000366" source-abbreviation="OBI"/>
5
+ <technology term-label="NMR spectroscopy" 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="extraction"/>
15
+ <field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false"
16
+ is-required="false" 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="NMR spectroscopy"/>
43
+ <field header="Parameter Value[instrument]" data-type="String" is-file-field="false" is-multiple-value="false"
44
+ is-required="false" is-hidden="false">
45
+ <description><![CDATA[the name of the NMR instrument]]></description>
46
+ <default-value><![CDATA[]]></default-value>
47
+ </field>
48
+ <field header="Parameter Value[NMR Probe]" data-type="String" is-file-field="false" is-multiple-value="false"
49
+ is-required="false" is-hidden="false">
50
+ <description><![CDATA[the type of probe fitted to the spectroscope]]></description>
51
+ <default-value><![CDATA[]]></default-value>
52
+ </field>
53
+ <field header="Parameter Value[number of acquisition]" data-type="String" is-file-field="false"
54
+ is-multiple-value="false" is-required="false" is-hidden="false">
55
+ <description>
56
+ <![CDATA[a parameter to indicate the number of acquisition used to generate the fid]]></description>
57
+ <default-value><![CDATA[]]></default-value>
58
+ </field>
59
+ <field header="Parameter Value[magnetic field strength]" data-type="String" is-file-field="false"
60
+ is-multiple-value="false" is-required="false" is-hidden="false">
61
+ <description><![CDATA[a parameter expressed in tesla to report the strength of the]]></description>
62
+ <default-value><![CDATA[]]></default-value>
63
+ </field>
64
+ <unit-field data-type="Ontology term" is-multiple-value="false" is-required="true">
65
+ <description>unit"</description>
66
+ </unit-field>
67
+ <field header="Acquisition Parameter Data File" data-type="String" is-file-field="true"
68
+ is-multiple-value="false" is-required="false" is-hidden="false">
69
+ <description>
70
+ <![CDATA[Name (or URI) of the acquisition parameter data file gathered for this assay.]]></description>
71
+ <default-value><![CDATA[]]></default-value>
72
+ </field>
73
+ <protocol-field protocol-type="nmr assay"/>
74
+ <field header="NMR Assay Name" data-type="String" is-file-field="false" is-multiple-value="false"
75
+ is-required="true" is-hidden="false">
76
+ <description><![CDATA[User-defined name for a NMR assay.]]></description>
77
+ <default-value><![CDATA[]]></default-value>
78
+ <generated-value-template>
79
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].NMRASSAY-[HYB_COUNT]
80
+ </generated-value-template>
81
+ </field>
82
+ <field header="Free Induction Decay Data File" data-type="String" is-file-field="true" is-multiple-value="false"
83
+ is-required="false" is-hidden="false">
84
+ <description>
85
+ <![CDATA[Name (or URI) of the free induction decay data file gathered for this assay.]]></description>
86
+ <default-value><![CDATA[]]></default-value>
87
+ </field>
88
+ <protocol-field protocol-type="data normalization"/>
89
+ <field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false"
90
+ is-required="false" is-hidden="false">
91
+ <description><![CDATA[User-defined name for each normalization applied]]></description>
92
+ <default-value><![CDATA[]]></default-value>
93
+ </field>
94
+ <protocol-field protocol-type="data transformation"/>
95
+ <field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true"
96
+ is-required="false" is-hidden="false">
97
+ <description><![CDATA[User-defined name for each data transformation applied]]></description>
98
+ <default-value><![CDATA[]]></default-value>
99
+ </field>
100
+ <field header="Derived Spectral Data File" data-type="String" is-file-field="true" is-multiple-value="false"
101
+ is-required="false" is-hidden="false">
102
+ <description>
103
+ <![CDATA[Name (or URI) of the derived data file generated from spectral data by an assay.]]></description>
104
+ <default-value><![CDATA[]]></default-value>
105
+ </field>
106
+ <field header="Metabolite Assignment File" data-type="String" is-file-field="true" is-multiple-value="false"
107
+ is-required="false" is-hidden="false">
108
+ <description>
109
+ <![CDATA[Name (or URI) of the metabolite assignment file gathered for this assay.]]></description>
110
+ <default-value><![CDATA[]]></default-value>
111
+ </field>
112
+ <structured-field name="Factors"/>
113
+ </isatab-configuration>
114
+ </isatab-config-file>
data/java/config/isa_configurator/metagenome_seq.xml ADDED
@@ -0,0 +1 @@
1
+ <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>
data/java/config/isa_configurator/transcription_micro.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="transcription_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="transcription profiling" term-accession="0000424" 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 ="RNA 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="45788"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>
data/java/config/isa_configurator/transcription_rtpcr.xml ADDED
@@ -0,0 +1 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="transcription_rtpcr" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="transcription profiling" term-accession="0000424" source-abbreviation="OBI"/><technology term-label="real time PCR" 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 ="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 ="reverse transcribed pcr"/><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><protocol-field protocol-type ="data collection"/><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 ="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><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 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/transcription_seq.xml ADDED
@@ -0,0 +1,6 @@
1
+ <isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="transcription_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="transcription profiling" term-accession="0000424" 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]
2
+ </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>
3
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
4
+ </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 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>
5
+ [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]
6
+ </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/toxbank-investigation.gemspec ADDED
@@ -0,0 +1,29 @@
1
+ # -*- encoding: utf-8 -*-
2
+ $:.push File.expand_path("../lib", __FILE__)
3
+
4
+ Gem::Specification.new do |s|
5
+ s.name = "toxbank-investigation"
6
+ s.version = "0.0.2pre"
7
+ s.authors = ["Christoph Helma","Denis Gebele","Micha Rautenberg"]
8
+ s.email = ["helma@in-silico.ch","gebele@in-silico.ch","rautenenberg@in-silico.ch"]
9
+ s.homepage = "http://github.com/ToxBank/toxbank-investigation"
10
+ s.summary = %q{Toxbank investigation service}
11
+ s.description = %q{Toxbank investigation service}
12
+ s.license = 'GPL-3'
13
+ #s.platform = Gem::Platform::CURRENT
14
+
15
+ s.rubyforge_project = "toxbank-investigation"
16
+
17
+ s.files = `git ls-files`.split("\n")
18
+ s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n")
19
+ s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
20
+ #s.require_paths = ["lib"]
21
+ s.required_ruby_version = '>= 1.9.2'
22
+
23
+ # specify any dependencies here; for example:
24
+ s.add_runtime_dependency "opentox-server"
25
+
26
+ # external requirements
27
+ ["git", "zip", "java", "curl", "wget"].each{|r| s.requirements << r}
28
+ s.post_install_message = "Run toxbank-investigation-install to set up your service"
29
+ end