From 1d37043d6581bbb5e6448e52a299c82c65e3cade Mon Sep 17 00:00:00 2001 From: Alejandra Gonzalez-Beltran Date: Mon, 20 Jan 2014 15:47:57 +0000 Subject: [PATCH] Updating to latest version of BII-I-1 --- isatab files/BII-I-1/a_metabolome.txt | 224 +++++++++--------- isatab files/BII-I-1/a_microarray.txt | 30 +-- isatab files/BII-I-1/a_proteome.txt | 38 +-- isatab files/BII-I-1/a_transcriptome.txt | 98 ++++---- isatab files/BII-I-1/i_Investigation.txt | 60 +++-- .../test-data/BII-I-1/a_metabolome.txt | 224 +++++++++--------- .../test-data/BII-I-1/a_microarray.txt | 30 +-- .../test-data/BII-I-1/a_proteome.txt | 38 +-- .../test-data/BII-I-1/a_transcriptome.txt | 98 ++++---- .../test-data/BII-I-1/i_investigation.txt | 60 +++-- 10 files changed, 474 insertions(+), 426 deletions(-) diff --git a/isatab files/BII-I-1/a_metabolome.txt b/isatab files/BII-I-1/a_metabolome.txt index c7acfbac..4f9465c9 100644 --- a/isatab files/BII-I-1/a_metabolome.txt +++ b/isatab files/BII-I-1/a_metabolome.txt @@ -1,112 +1,112 @@ -"Sample Name" "Material Type" "Term Source REF" "Term Accession Number" "Protocol REF" "Parameter Value[standard volume]" "Unit" "Term Source REF" "Term Accession Number" "Parameter Value[sample volume]" "Unit" "Term Source REF" "Term Accession Number" "Extract Name" "MS Assay Name" "Raw Spectral Data File" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"C-0.1-aliquot1" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.2-aliquot8" "JIC36_Sulphate_0.20_Internal_1_3" "JIC36_Sulphate_0.20_Internal_1_3.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hour" "" "" -"S-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_1" "JIC82_Sulphate_0.07_External_1_1.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot6" "JIC83_Sulphate_0.07_External_2_1" "JIC83_Sulphate_0.07_External_2_1.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.07-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" 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phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" +"P-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot6" "JIC73_Phosphate_0.07_External_1_2" "JIC73_Phosphate_0.07_External_1_2.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" +"P-0.07-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot7" "JIC73_Phosphate_0.07_External_1_3" "JIC73_Phosphate_0.07_External_1_3.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" +"P-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot5" "JIC74_Phosphate_0.07_External_2_1" "JIC74_Phosphate_0.07_External_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" +"P-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot5" "JIC75_Phosphate_0.07_External_3_1" "JIC75_Phosphate_0.07_External_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" +"P-0.1-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot5" "JIC76_Phosphate_0.10_External_1_1" "JIC76_Phosphate_0.10_External_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" +"P-0.1-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot6" "JIC77_Phosphate_0.10_External_2_1" "JIC77_Phosphate_0.10_External_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" +"P-0.1-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot7" "JIC78_Phosphate_0.10_External_3_1" "JIC78_Phosphate_0.10_External_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" +"P-0.2-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot5" "JIC79_Phosphate_0.20_External_1_1" "JIC79_Phosphate_0.20_External_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"P-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot6" "JIC80_Phosphate_0.20_External_2_1" "JIC80_Phosphate_0.20_External_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"P-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot7" "JIC81_Phosphate_0.20_External_3_1" "JIC81_Phosphate_0.20_External_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"N-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot5" "JIC64_Nitrogen_0.07_External_1_1" "JIC64_Nitrogen_0.07_External_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot5" "JIC64_Nitrogen_0.07_External_1_2" "JIC64_Nitrogen_0.07_External_1_2.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot5" "JIC64_Nitrogen_0.07_External_1_3" "JIC64_Nitrogen_0.07_External_1_3.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot6" "JIC65_Nitrogen_0.07_External_2_1" "JIC65_Nitrogen_0.07_External_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot7" "JIC66_Nitrogen_0.07_External_3_1" "JIC66_Nitrogen_0.07_External_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.1-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.1-aliquot5" "JIC67_Nitrogen_0.10_External_1_1" "JIC67_Nitrogen_0.10_External_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" +"N-0.1-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.1-aliquot6" "JIC68_Nitrogen_0.10_External_2_1" "JIC68_Nitrogen_0.10_External_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" +"N-0.1-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.1-aliquot7" "JIC69_Nitrogen_0.10_External_3_1" "JIC69_Nitrogen_0.10_External_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" +"N-0.2-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot5" "JIC70_Nitrogen_0.20_External_1_1" "JIC70_Nitrogen_0.20_External_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"N-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot6" "JIC71_Nitrogen_0.20_External_2_1" "JIC71_Nitrogen_0.20_External_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"N-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot7" "JIC72_Nitrogen_0.20_External_3_1" "JIC72_Nitrogen_0.20_External_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_1" "JIC55_Carbon_0.07_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_2" "JIC55_Carbon_0.07_External_1_2.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_3" "JIC55_Carbon_0.07_External_1_3.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot6" "JIC56_Carbon_0.07_External_2_1" "JIC56_Carbon_0.07_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot7" "JIC57_Carbon_0.07_External_3_1" "JIC57_Carbon_0.07_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.1-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot5" "JIC58_Carbon_0.10_External_1_1" "JIC58_Carbon_0.10_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.1-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot6" "JIC59_Carbon_0.10_External_2_1" "JIC59_Carbon_0.10_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.1-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot7" "JIC60_Carbon_0.10_External_3_1" "JIC60_Carbon_0.10_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.2-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot5" "JIC61_Carbon_0.20_External_1_1" "JIC61_Carbon_0.20_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"C-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot6" "JIC62_Carbon_0.20_External_2_1" "JIC62_Carbon_0.20_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"C-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot7" "JIC63_Carbon_0.20_External_3_1" "JIC63_Carbon_0.20_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"G-0.07-aliquot1" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.07-aliquot1" "JIC100_GlucoseO2_0.07_External_1_1" "JIC100_GlucoseO2_0.07_External_1_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.07" "l/hr" "" "" +"G-0.07-aliquot1" "extracellular region part" "CL" 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"NZ_0hrs_Sample_2_Labelled_Hyb2" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_0hrs_Sample_2_Labelled_Hyb2_Scan2" "E-MAXD-4-raw-data-426648675.txt" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "0" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "" "" "" -"NZ_1hrs_Grow2_Drug_Sample_2" "mRNA extraction" "NZ_1hrs_Drug_Sample_2_Extract" "biotin labeling" "NZ_1hrs_Drug_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_1hrs_Drug_Sample_2_Labelled_Hyb4" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_1hrs_Drug_Sample_2_Labelled_Hyb4_Scan4" "E-MAXD-4-raw-data-426648693.txt" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_4hrs_Grow2_Drug_Sample_2" "mRNA extraction" "NZ_4hrs_Drug_Sample_2_Extract" "biotin labeling" "NZ_4hrs_Drug_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Drug_Sample_2_Labelled_Hyb12" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Drug_Sample_2_Labelled_Hyb12_Scan12" "E-MAXD-4-raw-data-426648729.txt" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_2hrs_Grow2_Drug_Sample_2" "mRNA extraction" "NZ_2hrs_Drug_Sample_2_Extract" "biotin labeling" "NZ_2hrs_Drug_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Drug_Sample_2_Labelled_Hyb8" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Drug_Sample_2_Labelled_Hyb8_Scan8" 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"NZ_2hrs_Vehicle_Sample_2_Extract" "biotin labeling" "NZ_2hrs_Vehicle_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Vehicle_Sample_2_Labelled_Hyb10" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Vehicle_Sample_2_Labelled_Hyb10_Scan10" "E-MAXD-4-raw-data-426648765.txt" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_4hrs_Grow2_Vehicle_Sample_2" "mRNA extraction" "NZ_4hrs_Vehicle_Sample_2_Extract" "biotin labeling" "NZ_4hrs_Vehicle_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14_Scan14" "E-MAXD-4-raw-data-426648783.txt" "data processing" 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"NZ_4hrs_Drug_Sample_1_Labelled_Hyb11" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Drug_Sample_1_Labelled_Hyb11_Scan11" "E-MAXD-4-raw-data-426648603.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" +"NZ_2hrs_Grow1_Vehicle_Sample_1" "mRNA extraction" "NZ_2hrs_Vehicle_Sample_1_Extract" "biotin labeling" "NZ_2hrs_Vehicle_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Vehicle_Sample_1_Labelled_Hyb9" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Vehicle_Sample_1_Labelled_Hyb9_Scan9" "E-MAXD-4-raw-data-426648639.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" +"NZ_4hrs_Grow1_Vehicle_Sample_1" "mRNA extraction" "NZ_4hrs_Vehicle_Sample_1_Extract" "biotin labeling" "NZ_4hrs_Vehicle_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Vehicle_Sample_1_Labelled_Hyb13" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Vehicle_Sample_1_Labelled_Hyb13_Scan13" "E-MAXD-4-raw-data-426648657.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" +"NZ_1hrs_Grow1_Vehicle_Sample_1" "mRNA extraction" "NZ_1hrs_Vehicle_Sample_1_Extract" "biotin labeling" "NZ_1hrs_Vehicle_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_1hrs_Vehicle_Sample_1_Labelled_Hyb5" 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files/BII-I-1/a_proteome.txt @@ -1,19 +1,19 @@ -"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "MS Assay Name" "Comment[PRIDE Accession]" "Comment[PRIDE Processed Data Accession]" "Raw Spectral Data File" "Normalization Name" "Protein Assignment File" "Peptide Assignment File" "Post Translational Modification Assignment File" "Data Transformation Name" "Derived Spectral Data File" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"S-0.1-aliquot11" "protein extraction" "S-0.1" "ITRAQ labeling" "JC_S-0.1" "iTRAQ reagent 117" "" "" "8761" "8761" "8761" "spectrum.mzdata" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hr" "" "" -"C-0.1-aliquot11" "protein extraction" "C-0.1" 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"HYB:MEXP:3946" "A-AFFY-27" "SCAN:MEXP:3946" "E-MEXP-115-raw-data-331223977.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" +"S-0.07-aliquot4" "mRNA extraction" "S-0.07-aliquot4" "biotin labeling" "S-0.07-aliquot4" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3943" "A-AFFY-27" "SCAN:MEXP:3943" "E-MEXP-115-raw-data-331223501.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" +"S-0.1-aliquot1" "mRNA extraction" "S-0.1-aliquot1" "biotin labeling" "S-0.1-aliquot1" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3948" "A-AFFY-27" "SCAN:MEXP:3948" "E-MEXP-115-raw-data-331224301.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hr" "" "" +"S-0.1-aliquot2" "mRNA extraction" "S-0.1-aliquot2" "biotin labeling" "S-0.1-aliquot2" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3947" "A-AFFY-27" "SCAN:MEXP:3947" "E-MEXP-115-raw-data-331224145.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hr" "" "" +"S-0.1-aliquot3" "mRNA extraction" "S-0.1-aliquot3" "biotin labeling" "S-0.1-aliquot3" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3950" "A-AFFY-27" "SCAN:MEXP:3950" "E-MEXP-115-raw-data-331224703.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hr" "" "" +"S-0.1-aliquot4" "mRNA extraction" "S-0.1-aliquot4" "biotin labeling" "S-0.1-aliquot4" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3949" "A-AFFY-27" "SCAN:MEXP:3949" "E-MEXP-115-raw-data-331224480.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hr" "" "" +"S-0.2-aliquot1" "mRNA extraction" "S-0.2-aliquot1" "biotin labeling" "S-0.2-aliquot1" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3951" "A-AFFY-27" "SCAN:MEXP:3951" "E-MEXP-115-raw-data-331224884.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" +"S-0.2-aliquot2" "mRNA extraction" "S-0.2-aliquot2" "biotin labeling" "S-0.2-aliquot2" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3954" "A-AFFY-27" "SCAN:MEXP:3954" "E-MEXP-115-raw-data-331225401.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" +"S-0.2-aliquot3" "mRNA extraction" "S-0.2-aliquot3" "biotin labeling" "S-0.2-aliquot3" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3952" "A-AFFY-27" "SCAN:MEXP:3952" "E-MEXP-115-raw-data-331225097.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" +"S-0.2-aliquot4" "mRNA extraction" "S-0.2-aliquot4" "biotin labeling" "S-0.2-aliquot4" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3953" "A-AFFY-27" "SCAN:MEXP:3953" "E-MEXP-115-raw-data-331225235.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" diff --git a/isatab files/BII-I-1/i_Investigation.txt b/isatab files/BII-I-1/i_Investigation.txt index b3396128..463faf37 100644 --- a/isatab files/BII-I-1/i_Investigation.txt +++ b/isatab files/BII-I-1/i_Investigation.txt @@ -1,20 +1,21 @@ ONTOLOGY SOURCE REFERENCE -Term Source Name "" "OBI" "OBI_BCGO" "NCBITAXON" "CL" "e.g. OBI" "CHEBI" "RID" "EHDAA" "EFO" "FYPO" "BTO" "NEWT" "UO" "PATO" -Term Source File "" "" "http://data.bioontology.org/ontologies/OBI_BCGO" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/CL" "" "http://bioportal.bioontology.org/ontologies/49736" "http://bioportal.bioontology.org/ontologies/49816" "http://bioportal.bioontology.org/ontologies/45254" "http://bioportal.bioontology.org/ontologies/49794" "http://bioportal.bioontology.org/ontologies/49892" "ArrayExpress Experimental Factor Ontology" "" "" "" -Term Source Version "" "" "7" "2" "43" "" "49736" "49816" "45254" "49794" "49892" "v 1.26" "v 1.26" "v 1.26" "v 1.26" -Term Source Description "" "" "Beta Cell Genomics Ontology" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Cell Ontology" "" "Chemical entities of biological interest" "RadLex" "Human developmental anatomy, abstract version" "Experimental Factor Ontology" "Fission Yeast Phenotype Ontology" "BRENDA tissue / enzyme source" "NEWT UniProt Taxonomy Database" "Unit Ontology" "Phenotypic qualities (properties)" +Term Source Name "CHEBI" "CL" "OBI" "NCBITAXON" "OBI_BCGO" "PATO" "UO" +Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/CL" "http://data.bioontology.org/ontologies/OBI" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/OBI_BCGO" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/UO" +Term Source Version "78" "43" "21" "2" "8" "160" "42" +Term Source Description "Chemical Entities of Biological Interest Ontology" "Cell Ontology" "Ontology for Biomedical Investigations" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Beta Cell Genomics Ontology" "Phenotypic Quality Ontology" "Units of Measurement Ontology" INVESTIGATION Investigation Identifier "BII-I-1" Investigation Title "Growth control of the eukaryote cell: a systems biology study in yeast" Investigation Description "Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell." Investigation Submission Date "2007-04-30" Investigation Public Release Date "2009-03-10" -Comment [Created with configuration] "" -Comment [Last Opened With Configuration] "isaconfig-default_v2013-02-13-augmentedGigaDB" -Comment [Owning Organisation URI] "" -Comment [Consortium URI] "" -Comment [Principal Investigator URI] "" -Comment [Investigation keywords] "" +Comment[Created with configuration] "" +Comment[Last Opened With Configuration] "" +Comment[Created With Configuration] "" +Comment[Owning Organisation URI] "" +Comment[Consortium URI] "" +Comment[Principal Investigator URI] "" +Comment[Investigation Keywords] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "17439666" "1231222" "1234121" Investigation Publication DOI "doi:10.1186/jbiol54" "" "" @@ -36,15 +37,24 @@ Investigation Person Roles "corresponding author" "author" "author" Investigation Person Roles Term Accession Number "" "" "" Investigation Person Roles Term Source REF "" "" "" Comment[Investigation Person REF] "" "" "" +Comment[Investigation Person ORCID] "" "" "" STUDY Study Identifier "BII-S-1" +Study File Name "s_BII-S-1.txt" Study Title "Study of the impact of changes in flux on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae under different nutrient limitations" Study Description "We wished to study the impact of growth rate on the total complement of mRNA molecules, proteins, and metabolites in S. cerevisiae, independent of any nutritional or other physiological effects. To achieve this, we carried out our analyses on yeast grown in steady-state chemostat culture under four different nutrient limitations (glucose, ammonium, phosphate, and sulfate) at three different dilution (that is, growth) rates (D = u = 0.07, 0.1, and 0.2/hour, equivalent to population doubling times (Td) of 10 hours, 7 hours, and 3.5 hours, respectively; u = specific growth rate defined as grams of biomass generated per gram of biomass present per unit time)." -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" Study Submission Date "2007-04-30" Study Public Release Date "2009-03-10" -Study File Name "s_BII-S-1.txt" +Comment[Manuscript Licence] "CC BY 3.0" +Comment[Experimental Metadata Licence] "CC0" +Comment[Data Repository] "" +Comment[Data Record Accession] "" +Comment[Data Record URI] "" +Comment[Supplementary Information File Name] "" +Comment[Supplementary Information File Type] "" +Comment[Supplementary File URI] "" +Comment[Study Grant Number] "" +Comment[Study Funding Agency] "" STUDY DESIGN DESCRIPTORS Study Design Type "intervention design" Study Design Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000115" @@ -98,16 +108,27 @@ Study Person Affiliation "Faculty of Life Sciences, Michael Smith Building, Univ Study Person Roles "corresponding author" "author" "author" Study Person Roles Term Accession Number "" "" "" Study Person Roles Term Source REF "" "" "" -Comment[Study Person REF] "" "" "" +Comment[Study Person ORCID] "" "" "" +Comment[Funder] "" "" "" +Comment[FundRef ID] "" "" "" +Comment[Grant Identifier] "" "" "" STUDY Study Identifier "BII-S-2" +Study File Name "s_BII-S-2.txt" Study Title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" Study Description "Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. Gene expression at the mRNA level was investigated by transcriptome analysis using Affymetrix hybridization arrays." -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" Study Submission Date "2007-04-30" Study Public Release Date "2009-03-10" -Study File Name "s_BII-S-2.txt" +Comment[Manuscript Licence] "CC BY 3.0" +Comment[Experimental Metadata Licence] "CC0" +Comment[Data Repository] "" +Comment[Data Record Accession] "" +Comment[Data Record URI] "" +Comment[Supplementary Information File Name] "" +Comment[Supplementary Information File Type] "" +Comment[Supplementary File URI] "" +Comment[Study Grant Number] "" +Comment[Study Funding Agency] "" STUDY DESIGN DESCRIPTORS Study Design Type "time series design" Study Design Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0500020" @@ -161,4 +182,7 @@ Study Person Affiliation "Faculty of Life Sciences, Michael Smith Building, Univ Study Person Roles "corresponding author" "author" "author" Study Person Roles Term Accession Number "" "" "" Study Person Roles Term Source REF "" "" "" -Comment[Study Person REF] "" "" "" +Comment[Study Person ORCID] "" "" "" +Comment[Funder] "" "" "" +Comment[FundRef ID] "" "" "" +Comment[Grant Identifier] "" "" "" diff --git a/src/test/resources/test-data/BII-I-1/a_metabolome.txt b/src/test/resources/test-data/BII-I-1/a_metabolome.txt index c7acfbac..4f9465c9 100644 --- a/src/test/resources/test-data/BII-I-1/a_metabolome.txt +++ b/src/test/resources/test-data/BII-I-1/a_metabolome.txt @@ -1,112 +1,112 @@ -"Sample Name" "Material Type" "Term Source REF" "Term Accession Number" "Protocol REF" "Parameter Value[standard volume]" "Unit" "Term Source REF" "Term Accession Number" "Parameter Value[sample volume]" "Unit" "Term Source REF" "Term Accession Number" "Extract Name" "MS Assay Name" "Raw Spectral Data File" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"C-0.1-aliquot1" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.2-aliquot8" "JIC36_Sulphate_0.20_Internal_1_3" "JIC36_Sulphate_0.20_Internal_1_3.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hour" "" "" -"S-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_1" "JIC82_Sulphate_0.07_External_1_1.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot6" "JIC83_Sulphate_0.07_External_2_1" "JIC83_Sulphate_0.07_External_2_1.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.07-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot7" "JIC84_Sulphate_0.07_External_3_1" "JIC84_Sulphate_0.07_External_3_1.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_2" "JIC82_Sulphate_0.07_External_1_2.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_3" "JIC82_Sulphate_0.07_External_1_3.txt" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.07" "l/hr" "" "" -"S-0.1-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.1-aliquot5" "JIC85_Sulphate_0.10_External_1_1" 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"http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot9" "JIC21_Phosphate_0.07_Internal_2_1" "JIC21_Phosphate_0.07_Internal_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" +"P-0.1-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot8" "JIC22_Phosphate_0.10_Internal_1_1" "JIC22_Phosphate_0.10_Internal_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" +"P-0.1-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot9" "JIC23_Phosphate_0.10_Internal_2_1" "JIC23_Phosphate_0.10_Internal_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" +"P-0.1-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot10" "JIC24_Phosphate_0.10_Internal_3_1" "JIC24_Phosphate_0.10_Internal_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" +"P-0.2-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot8" "JIC25_Phosphate_0.20_Internal_1_1" "JIC25_Phosphate_0.20_Internal_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"P-0.2-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot9" "JIC26_Phosphate_0.20_Internal_2_1" "JIC26_Phosphate_0.20_Internal_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"P-0.2-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot10" "JIC27_Phosphate_0.20_Internal_3_1" "JIC27_Phosphate_0.20_Internal_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"N-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot8" "JIC10_Nitrogen_0.07_Internal_1_1" "JIC10_Nitrogen_0.07_Internal_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot8" "JIC10_Nitrogen_0.07_Internal_1_2" "JIC10_Nitrogen_0.07_Internal_1_2.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot8" "JIC10_Nitrogen_0.07_Internal_1_3" "JIC10_Nitrogen_0.07_Internal_1_3.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot9" "JIC11_Nitrogen_0.07_Internal_2_1" "JIC11_Nitrogen_0.07_Internal_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot10" "JIC12_Nitrogen_0.07_Internal_3_1" "JIC12_Nitrogen_0.07_Internal_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.1-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.1-aliquot8" "JIC13_Nitrogen_0.10_Internal_1_1" "JIC13_Nitrogen_0.10_Internal_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" +"N-0.1-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.1-aliquot9" "JIC14_Nitrogen_0.10_Internal_2_1" "JIC14_Nitrogen_0.10_Internal_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" +"N-0.1-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.1-aliquot10" "JIC15_Nitrogen_0.10_Internal_3_1" "JIC15_Nitrogen_0.10_Internal_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" +"N-0.2-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot8" "JIC16_Nitrogen_0.20_Internal_1_1" "JIC16_Nitrogen_0.20_Internal_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"N-0.2-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot9" "JIC17_Nitrogen_0.20_Internal_2_1" "JIC17_Nitrogen_0.20_Internal_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"N-0.2-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot10" "JIC18_Nitrogen_0.20_Internal_3_1" "JIC18_Nitrogen_0.20_Internal_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"C-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot8" "JIC1_Carbon_0.07_Internal_1_1" "JIC1_Carbon_0.07_Internal_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot8" "JIC1_Carbon_0.07_Internal_1_2" "JIC1_Carbon_0.07_Internal_1_2.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot8" "JIC1_Carbon_0.07_Internal_1_3" "JIC1_Carbon_0.07_Internal_1_3.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot9" "JIC2_Carbon_0.07_Internal_2_1" "JIC2_Carbon_0.07_Internal_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot10" "JIC3_Carbon_0.07_Internal_3_1" "JIC3_Carbon_0.07_Internal_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.1-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot8" "JIC4_Carbon_0.10_Internal_1_1" "JIC4_Carbon_0.10_Internal_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.1-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot9" "JIC5_Carbon_0.10_Internal_2_1" "JIC5_Carbon_0.10_Internal_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.1-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot10" "JIC6_Carbon_0.10_Internal_3_1" "JIC6_Carbon_0.10_Internal_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.2-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot8" "JIC7_Carbon_0.20_Internal_1_1" "JIC7_Carbon_0.20_Internal_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"C-0.2-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot9" "JIC8_Carbon_0.20_Internal_2_1" "JIC8_Carbon_0.20_Internal_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"C-0.2-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot10" "JIC9_Carbon_0.20_Internal_3_1" "JIC9_Carbon_0.20_Internal_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"G-0.07-aliquot4" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.07-aliquot4" "JIC46_GlucoseO2_0.07_Internal_1_1" "JIC46_GlucoseO2_0.07_Internal_1_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.07" "l/hr" "" "" +"G-0.07-aliquot4" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" 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"http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" +"N-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot5" "JIC64_Nitrogen_0.07_External_1_1" "JIC64_Nitrogen_0.07_External_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot5" "JIC64_Nitrogen_0.07_External_1_2" "JIC64_Nitrogen_0.07_External_1_2.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" +"N-0.07-aliquot5" "extracellular region 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"JIC70_Nitrogen_0.20_External_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"N-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot6" "JIC71_Nitrogen_0.20_External_2_1" "JIC71_Nitrogen_0.20_External_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"N-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot7" "JIC72_Nitrogen_0.20_External_3_1" "JIC72_Nitrogen_0.20_External_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" +"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_1" "JIC55_Carbon_0.07_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_2" "JIC55_Carbon_0.07_External_1_2.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" +"C-0.07-aliquot5" "extracellular region part" "CL" 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"C-0.1-aliquot6" "JIC59_Carbon_0.10_External_2_1" "JIC59_Carbon_0.10_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.1-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot7" "JIC60_Carbon_0.10_External_3_1" "JIC60_Carbon_0.10_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" +"C-0.2-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot5" "JIC61_Carbon_0.20_External_1_1" "JIC61_Carbon_0.20_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"C-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot6" "JIC62_Carbon_0.20_External_2_1" "JIC62_Carbon_0.20_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"C-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot7" "JIC63_Carbon_0.20_External_3_1" "JIC63_Carbon_0.20_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" +"G-0.07-aliquot1" "extracellular region part" "CL" 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b/src/test/resources/test-data/BII-I-1/a_microarray.txt index 6027228c..23a36f92 100644 --- a/src/test/resources/test-data/BII-I-1/a_microarray.txt +++ b/src/test/resources/test-data/BII-I-1/a_microarray.txt @@ -1,15 +1,15 @@ -"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "Protocol REF" "Hybridization Assay Name" "Comment[ArrayExpress Accession]" "Comment[ArrayExpress Raw Data URL]" "Comment[ArrayExpress Processed Data URL]" "Array Design REF" "Scan Name" "Array Data File" "Data Transformation Name" "Derived Array Data File" "Factor Value[dose]" "Unit" "Term Source REF" "Term Accession Number" "Factor Value[exposure time]" "Unit" "Term Source REF" "Term Accession Number" "Factor Value[compound]" "Term Source REF" "Term Accession Number" -"NZ_0hrs_Grow1_Sample_1" "mRNA extraction" "NZ_0hrs_Sample_1_Extract" "biotin labeling" "NZ_0hrs_Sample_1_Labelled" "biotin" "CHEBI" 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"EukGE-WS4" "NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14_Scan14" "E-MAXD-4-raw-data-426648783.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" diff --git a/src/test/resources/test-data/BII-I-1/a_proteome.txt b/src/test/resources/test-data/BII-I-1/a_proteome.txt index ff906e1e..a6894d46 100644 --- a/src/test/resources/test-data/BII-I-1/a_proteome.txt +++ b/src/test/resources/test-data/BII-I-1/a_proteome.txt @@ -1,19 +1,19 @@ -"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "MS Assay Name" "Comment[PRIDE Accession]" "Comment[PRIDE Processed Data Accession]" "Raw Spectral Data File" "Normalization Name" "Protein 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"A-AFFY-27" "SCAN:MEXP:3952" "E-MEXP-115-raw-data-331225097.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" +"S-0.2-aliquot4" "mRNA extraction" "S-0.2-aliquot4" "biotin labeling" "S-0.2-aliquot4" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3953" "A-AFFY-27" "SCAN:MEXP:3953" "E-MEXP-115-raw-data-331225235.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" diff --git a/src/test/resources/test-data/BII-I-1/i_investigation.txt b/src/test/resources/test-data/BII-I-1/i_investigation.txt index b3396128..463faf37 100644 --- a/src/test/resources/test-data/BII-I-1/i_investigation.txt +++ b/src/test/resources/test-data/BII-I-1/i_investigation.txt @@ -1,20 +1,21 @@ ONTOLOGY SOURCE REFERENCE -Term Source Name "" "OBI" "OBI_BCGO" "NCBITAXON" "CL" "e.g. OBI" "CHEBI" "RID" "EHDAA" "EFO" "FYPO" "BTO" "NEWT" "UO" "PATO" -Term Source File "" "" "http://data.bioontology.org/ontologies/OBI_BCGO" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/CL" "" "http://bioportal.bioontology.org/ontologies/49736" "http://bioportal.bioontology.org/ontologies/49816" "http://bioportal.bioontology.org/ontologies/45254" "http://bioportal.bioontology.org/ontologies/49794" "http://bioportal.bioontology.org/ontologies/49892" "ArrayExpress Experimental Factor Ontology" "" "" "" -Term Source Version "" "" "7" "2" "43" "" "49736" "49816" "45254" "49794" "49892" "v 1.26" "v 1.26" "v 1.26" "v 1.26" -Term Source Description "" "" "Beta Cell Genomics Ontology" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Cell Ontology" "" "Chemical entities of biological interest" "RadLex" "Human developmental anatomy, abstract version" "Experimental Factor Ontology" "Fission Yeast Phenotype Ontology" "BRENDA tissue / enzyme source" "NEWT UniProt Taxonomy Database" "Unit Ontology" "Phenotypic qualities (properties)" +Term Source Name "CHEBI" "CL" "OBI" "NCBITAXON" "OBI_BCGO" "PATO" "UO" +Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/CL" "http://data.bioontology.org/ontologies/OBI" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/OBI_BCGO" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/UO" +Term Source Version "78" "43" "21" "2" "8" "160" "42" +Term Source Description "Chemical Entities of Biological Interest Ontology" "Cell Ontology" "Ontology for Biomedical Investigations" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Beta Cell Genomics Ontology" "Phenotypic Quality Ontology" "Units of Measurement Ontology" INVESTIGATION Investigation Identifier "BII-I-1" Investigation Title "Growth control of the eukaryote cell: a systems biology study in yeast" Investigation Description "Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell." Investigation Submission Date "2007-04-30" Investigation Public Release Date "2009-03-10" -Comment [Created with configuration] "" -Comment [Last Opened With Configuration] "isaconfig-default_v2013-02-13-augmentedGigaDB" -Comment [Owning Organisation URI] "" -Comment [Consortium URI] "" -Comment [Principal Investigator URI] "" -Comment [Investigation keywords] "" +Comment[Created with configuration] "" +Comment[Last Opened With Configuration] "" +Comment[Created With Configuration] "" +Comment[Owning Organisation URI] "" +Comment[Consortium URI] "" +Comment[Principal Investigator URI] "" +Comment[Investigation Keywords] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "17439666" "1231222" "1234121" Investigation Publication DOI "doi:10.1186/jbiol54" "" "" @@ -36,15 +37,24 @@ Investigation Person Roles "corresponding author" "author" "author" Investigation Person Roles Term Accession Number "" "" "" Investigation Person Roles Term Source REF "" "" "" Comment[Investigation Person REF] "" "" "" +Comment[Investigation Person ORCID] "" "" "" STUDY Study Identifier "BII-S-1" +Study File Name "s_BII-S-1.txt" Study Title "Study of the impact of changes in flux on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae under different nutrient limitations" Study Description "We wished to study the impact of growth rate on the total complement of mRNA molecules, proteins, and metabolites in S. cerevisiae, independent of any nutritional or other physiological effects. To achieve this, we carried out our analyses on yeast grown in steady-state chemostat culture under four different nutrient limitations (glucose, ammonium, phosphate, and sulfate) at three different dilution (that is, growth) rates (D = u = 0.07, 0.1, and 0.2/hour, equivalent to population doubling times (Td) of 10 hours, 7 hours, and 3.5 hours, respectively; u = specific growth rate defined as grams of biomass generated per gram of biomass present per unit time)." -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" Study Submission Date "2007-04-30" Study Public Release Date "2009-03-10" -Study File Name "s_BII-S-1.txt" +Comment[Manuscript Licence] "CC BY 3.0" +Comment[Experimental Metadata Licence] "CC0" +Comment[Data Repository] "" +Comment[Data Record Accession] "" +Comment[Data Record URI] "" +Comment[Supplementary Information File Name] "" +Comment[Supplementary Information File Type] "" +Comment[Supplementary File URI] "" +Comment[Study Grant Number] "" +Comment[Study Funding Agency] "" STUDY DESIGN DESCRIPTORS Study Design Type "intervention design" Study Design Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000115" @@ -98,16 +108,27 @@ Study Person Affiliation "Faculty of Life Sciences, Michael Smith Building, Univ Study Person Roles "corresponding author" "author" "author" Study Person Roles Term Accession Number "" "" "" Study Person Roles Term Source REF "" "" "" -Comment[Study Person REF] "" "" "" +Comment[Study Person ORCID] "" "" "" +Comment[Funder] "" "" "" +Comment[FundRef ID] "" "" "" +Comment[Grant Identifier] "" "" "" STUDY Study Identifier "BII-S-2" +Study File Name "s_BII-S-2.txt" Study Title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" Study Description "Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. Gene expression at the mRNA level was investigated by transcriptome analysis using Affymetrix hybridization arrays." -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" Study Submission Date "2007-04-30" Study Public Release Date "2009-03-10" -Study File Name "s_BII-S-2.txt" +Comment[Manuscript Licence] "CC BY 3.0" +Comment[Experimental Metadata Licence] "CC0" +Comment[Data Repository] "" +Comment[Data Record Accession] "" +Comment[Data Record URI] "" +Comment[Supplementary Information File Name] "" +Comment[Supplementary Information File Type] "" +Comment[Supplementary File URI] "" +Comment[Study Grant Number] "" +Comment[Study Funding Agency] "" STUDY DESIGN DESCRIPTORS Study Design Type "time series design" Study Design Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0500020" @@ -161,4 +182,7 @@ Study Person Affiliation "Faculty of Life Sciences, Michael Smith Building, Univ Study Person Roles "corresponding author" "author" "author" Study Person Roles Term Accession Number "" "" "" Study Person Roles Term Source REF "" "" "" -Comment[Study Person REF] "" "" "" +Comment[Study Person ORCID] "" "" "" +Comment[Funder] "" "" "" +Comment[FundRef ID] "" "" "" +Comment[Grant Identifier] "" "" ""