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Commit 722d2267 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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remove old helper files

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_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md deleted 100644 → 0
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| ASSAY METADATA | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 |
|:-----------------|:------------------------------|:----------------|:-------------|:-------------|:-------------|
| Measurement Type | GCqTOF targeted | | | | |
| File Name | GCqTOF_targets/isa.assay.xlsx | | | | |
| Last Name | Brilhaus | Mettler-Altmann | Klemp | Graf | Weber |
| First Name | Dominik | Tabea | Elisabeth | Maria | Katrin |
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_isa-md/assays/GCqTOF_targets/isa.assay/gas_chromatography.md deleted 100644 → 0
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| Source Name | Protocol REF | Protocol Type | Parameter [MS sample type] | Parameter [Chromatography instrument model] | Parameter [Chromatography autosampler model] | Parameter [Chromatography column type] | Parameter [Chromatography column model] | Parameter [mobile phase] | Parameter [Chromatography injection volume] | Unit | Parameter [Chromatography injection mode] | Parameter [Chromatography gradient] | Sample Name |
|:--------------|:----------------------|:----------------|:-----------------------------|:----------------------------------------------|:-----------------------------------------------|:-----------------------------------------|:------------------------------------------|:---------------------------|----------------------------------------------:|:-----------|:--------------------------------------------|:--------------------------------------|--------------:|
| Std. Mix 5µM | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-433 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_03 |
| Std. Mix 5µM | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-434 | helium(0) | 1 | microliter | split | gradient elution | 150112_04 |
| blank 1 | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-435 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_15 |
| blank 1 | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-436 | helium(0) | 1 | microliter | split | gradient elution | 150112_16 |
| DB23 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-437 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_55 |
| DB23 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-438 | helium(0) | 1 | microliter | split | gradient elution | 150112_56 |
| DB24 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-439 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_61 |
| DB24 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-440 | helium(0) | 1 | microliter | split | gradient elution | 150112_62 |
| DB26 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-441 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_65 |
| DB26 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-442 | helium(0) | 1 | microliter | split | gradient elution | 150112_66 |
| Std. Mix 5µM | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-443 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_03 |
| Std. Mix 5µM | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-444 | helium(0) | 1 | microliter | split | gradient elution | 150115_04 |
| DB39 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-445 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_11 |
| DB39 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-446 | helium(0) | 1 | microliter | split | gradient elution | 150115_12 |
| DB40 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-447 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_13 |
| DB40 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-448 | helium(0) | 1 | microliter | split | gradient elution | 150115_14 |
| DB41 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-449 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_15 |
| DB41 | gas_chromatography.md | assay protocol | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-450 | helium(0) | 1 | microliter | split | gradient elution | 150115_16 |
| blank 2 | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-451 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_25 |
| blank 2 | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-452 | helium(0) | 1 | microliter | split | gradient elution | 150115_26 |
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_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md deleted 100644 → 0
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| Source Name | Protocol Type | Protocol REF | Parameter [scan polarity] | Parameter [scan window lower limit] | Parameter [scan window upper limit] | Parameter [scan rate] | Unit | Parameter [instrument model] | Parameter [ionization type] | Parameter [mass analyzer type] | Parameter [detector type] | Data File Name |
|--------------:|:----------------|:---------------|:----------------------------|--------------------------------------:|--------------------------------------:|------------------------:|:-------|:------------------------------------|:------------------------------|:---------------------------------|:----------------------------|:-----------------|
| 150112_03 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_03.D |
| 150112_04 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_04.D |
| 150112_15 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_15.D |
| 150112_16 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_16.D |
| 150112_55 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_55.D |
| 150112_56 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_56.D |
| 150112_61 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_61.D |
| 150112_62 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_62.D |
| 150112_65 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_65.D |
| 150112_66 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_66.D |
| 150115_03 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_03.D |
| 150115_04 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_04.D |
| 150115_11 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_11.D |
| 150115_12 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_12.D |
| 150115_13 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_13.D |
| 150115_14 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_14.D |
| 150115_15 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_15.D |
| 150115_16 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_16.D |
| 150115_25 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_25.D |
| 150115_26 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_26.D |
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_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md deleted 100644 → 0
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| Source Name | Protocol Type | Protocol REF | Parameter [Bio entity] | Parameter [Biosource amount] | Unit (#2) | Parameter [Biosource material state] | Parameter [Extraction buffer] | Parameter [Extraction buffer volume] | Parameter [Internal standard] | Parameter [Sample volume] | Unit | Parameter [MS sample post-extraction] | Parameter [MS sample resuspension] | Parameter [MS derivatization] | Sample Name |
|:--------------|:--------------------|:-------------------------|:-------------------------|-------------------------------:|:------------|:---------------------------------------|:------------------------------------------|---------------------------------------:|:--------------------------------|----------------------------:|:-----------|:----------------------------------------|:-------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------|:--------------|
| CAM_01 | extraction protocol | metabolite_extraction.md | metabolites | 6.1 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | (1) with 10 μl methoxyamine hydrochloride (Acros organics; freshly prepared at 20 mg/ml in pure pyridine (Sigma-Aldrich)) and shaking at 37 ◦C | DB23 |
| | | | | | | | | | | | | | | for 90 min, (2) adding 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA; Macherey-Nagel) and shaking at 37 ◦C for 30 min. | |
| CAM_02 | extraction protocol | metabolite_extraction.md | metabolites | 5.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | 10 μl methoxyamine hydrochloride and 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide MSTFA | DB24 |
| CAM_03 | extraction protocol | metabolite_extraction.md | metabolites | 8.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | MaHCl and MSTFA | DB26 |
| reC3_01 | extraction protocol | metabolite_extraction.md | metabolites | 4.9 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | DB39 |
| reC3_02 | extraction protocol | metabolite_extraction.md | metabolites | 6 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | DB40 |
| reC3_03 | extraction protocol | metabolite_extraction.md | metabolites | 6.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | DB41 |
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_isa-md/assays/MassHunter_targets/isa.assay/Assay.md deleted 100644 → 0
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| ASSAY METADATA | Unnamed: 1 |
|:-----------------|:----------------------------------|
| File Name | MassHunter_targets/isa.assay.xlsx |
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_isa-md/assays/MassHunter_targets/isa.datapackage/Derivations.md deleted 100644 → 0
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| Identifier | TargetFile | wasDerivedFrom | Unnamed: 3 |
|:----------------|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------|
| Data File | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]05_metabolites_datatrans':Source Name | [./assays/GCqTOF_targets/isa.assay.xlsx]04_metabolites_massspec':Data File Name |
| Sample Name | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/GCqTOF_targets/isa.assay.xlsx]03_metabolites_chromatography':Source Name | |
| Sample.Type | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/GCqTOF_targets/isa.assay.xlsx]03_metabolites_chromatography':Parameter [MS sample type] | |
| Position | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Inj Vol | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Instrument | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Acq.Method.File | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| SpeedVacVol | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Sample.Comment | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Sample.Approved | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Compound | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| ISTD | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Resp | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| ISTD Resp | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| Resp Ratio | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| UserAnno.Peak | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| MI.Peak | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| MZ | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| MZ.Ex.Left | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| MZ.Ex.Right | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| MZ.Ex.Units | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| RT.Compound | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
| RT.Peak | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | | |
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_isa-md/assays/MassHunter_targets/isa.datapackage/Dictionary.md deleted 100644 → 0
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| Identifier | TargetFile | wasGeneratedBy | Attribute [Term] | Attribute | Unit | Comment |
|:----------------|:------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------|:---------------------------------------------------|:-------------------|:---------------------------------|:-------------------------------------------------------------------------|
| Data File | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | | ISA Data File Name | | |
| Sample Name | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | | ISA Sample Name | | |
| Sample.Type | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | MS sample type [NFDI4PSO:0000045] | MS sample type | | |
| Position | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Vial position | | | Indicates the vial position (e.g. in the autosampler) |
| Inj Vol | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Chromatography injection volume [NFDI4PSO:0010014] | | microliter [UO_0000101] | |
| Instrument | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | instrument model [MS:1000031] | | | |
| Acq.Method.File | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Acquisition Method File Name [User specific] | | | References the acquisition method used during GC-MS |
| SpeedVacVol | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Sample volume [NFDI4PSO:0010013] | | | |
| Sample.Comment | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Quality check comment [User specific] | | | QC comment of sample |
| Sample.Approved | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Quality check [User specific] | | | QC of sample |
| Compound | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Compound [NCIT_C43366] | | | |
| ISTD | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Internal standard | | | see http://purl.obolibrary.org/obo/MSIO_0000005 (internal standard role) |
| Resp | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | peak intensity [MS_1000042] | | area under curve [STATO_0000209] | peak intensity of the Compound |
| ISTD Resp | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | peak intensity [MS_1000042] | | | peak intensity of the ISTD |
| Resp Ratio | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | ratio [STATO_0000184] | | | ratio of peak intensities of (compound : ISTD) |
| UserAnno.Peak | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Quality check comment [User specific] | | | QC comment of peak intensity |
| MI.Peak | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | Quality check [User specific] | | | QC of peak intensity |
| MZ | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | m/z [MS_1000040] | | | mass-to-charge ratio of extracted ion |
| MZ.Ex.Left | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | isolation window lower offset [MS_1000828] | | | |
| MZ.Ex.Right | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | isolation window upper offset [MS_1000829] | | | |
| MZ.Ex.Units | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | | | | |
| RT.Compound | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | retention time [MS_1000894] | | | targeted retention time for compound |
| RT.Peak | ./assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx | [./assays/MassHunter_targets/isa.assay.xlsx]06_metabolites_identification' | retention time [MS_1000894] | | | actual retention time, at which the peak for the compound was extracted |
| | | | Add to NFDI4PSO | | | |
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| ASSAY METADATA | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 |
|:---------------------------------------|:------------------------------------------------------------------|:------------------------------------------------|:------------------------------------------------|:---------------------------------------------------|
| Measurement Type | mRNA Sequencing | | | |
| Measurement Type Term Accession Number | http://purl.obolibrary.org/obo/NCIT_C129432 | | | |
| Measurement Type Term Source REF | NCIT | | | |
| Technology Type | Next Generation Sequencing | | | |
| Technology Type Term Accession Number | http://purl.obolibrary.org/obo/NCIT_C101293 | | | |
| Technology Type Term Source REF | NCIT | | | |
| Technology Platform | Illumina HiSeq 2500 | | | |
| File Name | Talinum_RNASeq_minimal/isa.assay.xlsx | | | |
| Last Name | Brilhaus | Winter | Kurz | Wachtmeister |
| First Name | Dominik | Klaus | Samantha | Thorsten |
| Email | dominik.brilhaus@hhu.de | | | |
| Phone | 0211-8115523 | | | |
| Address | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Balboa, Ancón, Republic of Panama | Universitätsstr. 1, 40225 Düsseldorf | Universitätsstr. 1, 40225 Düsseldorf |
| Affiliation | Institute of Plant Biochemistry, HHU Düsseldorf | Smithsonian Tropical Research Institute, Panama | Institute of Plant Biochemistry, HHU Düsseldorf | Biological Medical Research Centre, HHU Düsseldorf |
| Roles | research assistant | co-investigator | technician | technician |
| Roles Term Accession Number | http://purl.org/spar/scoro/research-assistant | http://purl.org/spar/scoro/co-investigator | http://purl.org/spar/scoro/technician | http://purl.org/spar/scoro/technician |
| Roles Term Source REF | scoro | scoro | scoro | scoro |
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| Source Name | Protocol Type | Protocol REF | Parameter [library strategy] | Parameter [library selection] | Parameter [library layout] | Parameter [library preparation kit] | Parameter [library preparation kit version] | Parameter [adapter sequence] | Parameter [next generation sequencing instrument model] | Parameter [base-calling software] | Parameter [base-calling software version] | Parameter [Raw data file format] | Raw Data File |
|:--------------|:----------------|:---------------|:-------------------------------|:--------------------------------|:-----------------------------|:--------------------------------------|:----------------------------------------------|:-------------------------------|:----------------------------------------------------------|:------------------------------------|:--------------------------------------------|:-----------------------------------|:-------------------------------------------|
| CAM_01_ext | assay protocol | illumina.md | RNA-seq | cDNA method | single-end | Illumina TruSeq RNA Sample Prep Kit | version 2 | CAGATC | Illumina HiSeq 2000 | Illumina Cassava | v1.8.2 | *.fastq.gz | DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz |
| CAM_02_ext | assay protocol | illumina.md | RNA-seq | cDNA method | single-end | Illumina TruSeq RNA Sample Prep Kit | version 2 | CTTGTA | Illumina HiSeq 2000 | Illumina Cassava | v1.8.2 | *.fastq.gz | DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz |
| CAM_03_ext | assay protocol | illumina.md | RNA-seq | cDNA method | single-end | Illumina TruSeq RNA Sample Prep Kit | version 2 | AGTCAA | Illumina HiSeq 2000 | Illumina Cassava | v1.8.2 | *.fastq.gz | DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz |
| reC3_01_ext | assay protocol | illumina.md | RNA-seq | cDNA method | single-end | Illumina TruSeq RNA Sample Prep Kit | version 2 | GTCCGC | Illumina HiSeq 2000 | Illumina Cassava | v1.8.2 | *.fastq.gz | DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz |
| reC3_02_ext | assay protocol | illumina.md | RNA-seq | cDNA method | single-end | Illumina TruSeq RNA Sample Prep Kit | version 2 | GTGAAA | Illumina HiSeq 2000 | Illumina Cassava | v1.8.2 | *.fastq.gz | DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz |
| reC3_03_ext | assay protocol | illumina.md | RNA-seq | cDNA method | single-end | Illumina TruSeq RNA Sample Prep Kit | version 2 | GTGAAA | Illumina HiSeq 2000 | Illumina Cassava | v1.8.2 | *.fastq.gz | DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz |
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| Source Name | Protocol Type | Protocol REF | Parameter [biosource amount] | Unit | Parameter [extraction method] | Parameter [extraction buffer] | Parameter [extraction buffer volume] | Unit (#2) | Parameter [RNA quality check] | Sample Name |
|:--------------|:------------------------|:------------------|-------------------------------:|:----------|:-------------------------------------------------------------------------------|:--------------------------------|---------------------------------------:|:------------|:---------------------------------------------------------|:--------------|
| CAM_01 | RNA extraction protocol | rna_extraction.md | 80 | milligram | Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011 | Roboklon commercial buffers | 300 | microliter | RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano) | CAM_01_ext |
| CAM_02 | RNA extraction protocol | rna_extraction.md | 78 | milligram | Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011 | Roboklon commercial buffers | 300 | microliter | RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano) | CAM_02_ext |
| CAM_03 | RNA extraction protocol | rna_extraction.md | 93 | milligram | Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011 | Roboklon commercial buffers | 300 | microliter | RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano) | CAM_03_ext |
| reC3_01 | RNA extraction protocol | rna_extraction.md | 82 | milligram | Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011 | Roboklon commercial buffers | 300 | microliter | RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano) | reC3_01_ext |
| reC3_02 | RNA extraction protocol | rna_extraction.md | 96 | milligram | Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011 | Roboklon commercial buffers | 300 | microliter | RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano) | reC3_02_ext |
| reC3_03 | RNA extraction protocol | rna_extraction.md | 78 | milligram | Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011 | Roboklon commercial buffers | 300 | microliter | RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano) | reC3_03_ext |
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source diff could not be displayed: it is too large. Options to address this: view the blob.
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| Data Pointer | Data File Name | wasGeneratedBy | Attribute | ObjectType | Label | Comment |
|:----------------|:------------------------------------|:----------------------------|:-----------------------------|:-------------|:-----------------------------|:-------------------------------------------|
| target_id | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | gene identifier | String | Gene ID | Gene identifier, reference to fasta |
| pval | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | p-value | Decimal | P-Value | Pvalue, has a term |
| qval | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | q-value | Decimal | Q-Value | qVal, has a term |
| test_stat | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | test statistic | Decimal | Test Statistic | test statisitc, has a term |
| rss | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | residual | Decimal | Residual sum of squares | residual sum of squares, has a term |
| degrees_free | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | number of degrees of freedom | Integer | Number Of Degrees Of Freedom | degrees of freedom, has a term |
| mean_obs | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | mean | Decimal | Mean | mean of observations, needs references |
| var_obs | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | variance | Decimal | Variance | variance of observations, needs references |
| tech_var | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | variance | Decimal | Technical variance | technical variance? Has a term |
| sigma_sq | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | variance | Decimal | Variance | variance of observations, needs references |
| smooth_sigma_sq | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | smoothed variance | Decimal | Smoothed Variance | smoothed variance |
| final_sigma_sq | runs/kallisto_sleuth/sleuth_dge.csv | workflows/kallisto_sleuth.R | corrected variance | Decimal | Corrected Variance | adjusted variance |
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| Data Pointer | Data File Name | wasGeneratedBy | Attribute | ObjectType | Label | Comment |
|:----------------|:----------------------------------------|:--------------------------------------------|:-----------------------------|:-------------|:-----------------------------|:-------------------------------------------|
| target_id | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | gene identifier | String | Gene ID | Gene identifier, reference to fasta |
| pval | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | p-value | Decimal | P-Value | Pvalue, has a term |
| qval | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | q-value | Decimal | Q-Value | qVal, has a term |
| test_stat | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | test statistic | Decimal | Test Statistic | test statisitc, has a term |
| rss | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | residual | Decimal | Residual sum of squares | residual sum of squares, has a term |
| degrees_free | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | number of degrees of freedom | Integer | Number Of Degrees Of Freedom | degrees of freedom, has a term |
| mean_obs | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | mean | Decimal | Mean | mean of observations, needs references |
| var_obs | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | variance | Decimal | Variance | variance of observations, needs references |
| tech_var | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | variance | Decimal | Technical variance | technical variance? Has a term |
| sigma_sq | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | variance | Decimal | Variance | variance of observations, needs references |
| smooth_sigma_sq | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | smoothed variance | Decimal | Smoothed Variance | smoothed variance |
| final_sigma_sq | runs/kallisto_sleuth/out/sleuth_dge.csv | workflows/kallisto_sleuth/kallisto_sleuth.R | corrected variance | Decimal | Corrected Variance | adjusted variance |
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| STUDY METADATA | Unnamed: 1 | Unnamed: 2 |
|:-----------------------------------------|:------------------------------------------------------------------|:------------------------------------------------|
| Study Identifier | TalinumFacultativeCAM | |
| Study File Name | TalinumFacultativeCAM/isa.study.xlsx | |
| Study Person Last Name | Brilhaus | Winter |
| Study Person First Name | Dominik | Klaus |
| Study Person Email | dominik.brilhaus@hhu.de | |
| Study Person Phone | 0211-8115523 | |
| Study Person Address | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Balboa, Ancón, Republic of Panama |
| Study Person Affiliation | Institute of Plant Biochemistry, HHU Düsseldorf | Smithsonian Tropical Research Institute, Panama |
| Study Person Roles | research assistant | co-investigator |
| Study Person Roles Term Accession Number | http://purl.org/spar/scoro/research-assistant | http://purl.org/spar/scoro/co-investigator |
| Study Person Roles Term Source REF | scoro | scoro |
| Comment[<Study Person ORCID>] | http://orcid.org/0000-0001-9021-3197 | |
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| Source Name | Protocol REF | Protocol Type | Characteristic [organism] | Characteristic [organism part] | Characteristic [plant age] | Parameter [growth day length] | Parameter [light intensity exposure] | Unit | Parameter [humidity day] | Unit | Parameter [temperature day] | Unit | Parameter [temperature night] | Unit | Factor [watering exposure] | Factor [Timepoint] | Factor [timepoint-ZT] | Factor [Photosynthesis mode] | Sample Name |
|:--------------|:------------------|:----------------------|:----------------------------|:---------------------------------|:-----------------------------|:--------------------------------|---------------------------------------:|:------------------------------------------|---------------------------:|:--------|------------------------------:|:---------------|--------------------------------:|:---------------|:-----------------------------------|:---------------------|------------------------:|:-------------------------------|:--------------|
| DB_097 | plant_material.md | plant growth protocol | Talinum fruticosum | leaf | 28 days after germination | 12 hr light / 12 hr dark | 425 | microeinstein per square meter per second | 37 | percent | 30 | degree celsius | 22 | degree celsius | 12 days drought | MD | 6 | CAM | CAM_01 |
| DB_099 | plant_material.md | plant growth protocol | Talinum fruticosum | leaf | 28 days after germination | 12 hr light / 12 hr dark | 425 | microeinstein per square meter per second | 37 | percent | 30 | degree celsius | 22 | degree celsius | 12 days drought | MD | 6 | CAM | CAM_02 |
| DB_103 | plant_material.md | plant growth protocol | Talinum fruticosum | leaf | 28 days after germination | 12 hr light / 12 hr dark | 425 | microeinstein per square meter per second | 37 | percent | 30 | degree celsius | 22 | degree celsius | 12 days drought | MD | 6 | CAM | CAM_03 |
| DB_161 | plant_material.md | plant growth protocol | Talinum fruticosum | leaf | 28 days after germination | 12 hr light / 12 hr dark | 425 | microeinstein per square meter per second | 37 | percent | 30 | degree celsius | 22 | degree celsius | 12 days drought + 2 days rewatered | MD | 6 | reC3 | reC3_01 |
| DB_163 | plant_material.md | plant growth protocol | Talinum fruticosum | leaf | 28 days after germination | 12 hr light / 12 hr dark | 425 | microeinstein per square meter per second | 37 | percent | 30 | degree celsius | 22 | degree celsius | 12 days drought + 2 days rewatered | MD | 6 | reC3 | reC3_02 |
| DB_165 | plant_material.md | plant growth protocol | Talinum fruticosum | leaf | 28 days after germination | 12 hr light / 12 hr dark | 425 | microeinstein per square meter per second | 37 | percent | 30 | degree celsius | 22 | degree celsius | 12 days drought + 2 days rewatered | MD | 6 | reC3 | reC3_03 |
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| STUDY METADATA | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 |
|:-----------------------------------------|:------------------------------------------------|:------------------------------------------------------------------|:------------------------------------------------|:--------------------------------------------------|
| Study Identifier | TalinumGenomeDraft | | | |
| Study File Name | TalinumGenomeDraft/isa.study.xlsx | | | |
| Study Person Last Name | Maleckova | Brilhaus | Denton | Weber |
| Study Person First Name | Eva | Dominik | Alisandra | Andreas |
| Study Person Mid Initials | | | K | P M |
| Study Person Email | | dominik.brilhaus@hhu.de | | |
| Study Person Phone | | 0211-8115523 | | |
| Study Person Address | Universitätsstr. 1, 40225 Düsseldorf | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Universitätsstr. 1, 40225 Düsseldorf | Universitätsstr. 1, 40225 Düsseldorf |
| Study Person Affiliation | Institute of Plant Biochemistry, HHU Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf |
| Study Person Roles | research assistant | research assistant | research assistant | principal investigator |
| Study Person Roles Term Accession Number | http://purl.org/spar/scoro/research-assistant | http://purl.org/spar/scoro/research-assistant | http://purl.org/spar/scoro/research-assistant | http://purl.org/spar/scoro/principal-investigator |
| Study Person Roles Term Source REF | scoro | scoro | scoro | scoro |
| Comment[<Study Person ORCID>] | https://orcid.org/0000-0001-9062-3516 | http://orcid.org/0000-0001-9021-3197 | | http://orcid.org/0000-0003-0970-4672 |
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| Source Name | Derived Data File |
|:------------------------|:---------------------|
| VariousTalinumData[WIP] | Talinum.gm.CDS.nt.fa |
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# Small helper to auto-create an import for draw.io
folder | fill | stroke | shape
-------|------|--------|------
runs | #C21F3A | #2D3E69 | ellipse
assays | #FFC000 | #2D3E68 | rectangle
studies | #B4CE82 | #2D3E50 | rectangle
workflows | #4FB3D9 | #2D3E57 | rhombus
```bash
find runs -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"runs", "#C21F3A", "#2D3E69", "ellipse"}' | tr ' ' ',' > tmp.runs.columns.csv
find assays -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"assays", "#FFC000", "#2D3E69", "rectangle"}' | tr ' ' ',' > tmp.assays.columns.csv
find studies -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"studies", "#B4CE82", "#2D3E50", "rectangle"}' | tr ' ' ',' > tmp.studies.columns.csv
find workflows -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"workflows", "#4FB3D9", "#2D3E57", "rhombus"}' | tr ' ' ',' > tmp.workflows.columns.csv
## append rwo number
cat tmp.*.columns.csv | awk -F',' '{$0=$0","NR} 1' > tmp_drawioimport.csv
awk 'BEGIN{print "step,folder,fill,stroke,shape,id"} {print}' tmp_drawioimport.csv > drawioimport.csv
cat _workflow_scheme/drawioimport_header drawioimport.csv > drawioimport_ready
mv drawioimport* _workflow_scheme
rm tmp*
```
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