diff --git a/_isa-md/README.md b/_isa-md/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5b042ab2590eb927eb07a2de284e30489e1ea5fa --- /dev/null +++ b/_isa-md/README.md @@ -0,0 +1,14 @@ +# ISA Metadata as markdown tables + +:warning: This is just for convenience since .xlsx files are not shown in GitLab. Check the original `isa.*.xlsx` for latest metadata. + + +## Convert xlsx to md + +For convenience (i.e. since `.xlsx` are not shown in GitLab), I wrote a [little helper tool](https://github.com/nfdi4plants/xlsx2markdownTable) that converts all xlsx into markdown tables. + +```bash +xlsx2md -e "isa" -o _isa-md -d -di +``` + +:bulb: This collects all "isa" metadata it will find in a separate folder (in root). \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md b/_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md new file mode 100644 index 0000000000000000000000000000000000000000..08d18351b7774dac8fe6fd812835cca2e6f71186 --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md @@ -0,0 +1,9 @@ +| Source Name | 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] | Parameter [label] | Sample Name | +|:--------------|:-------------------------|-------------------------------:|:------------|:---------------------------------------|:------------------------------------------|---------------------------------------:|:--------------------------------|----------------------------:|:-----------|:----------------------------------------|:-------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------|:--------------------|:--------------| +| CAM_01 | 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 | 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 | 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 | 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 | 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 | 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 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md b/_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md new file mode 100644 index 0000000000000000000000000000000000000000..d822c9c4a7b9b916fe87bdd2a68e5441b08e7b2b --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md @@ -0,0 +1,22 @@ +| Source Name | Parameter [MS sample type] | Parameter [Chromatography instrument model] | Parameter [Chromatography autosampler model] | Parameter [Chromatography column type] | Parameter [Chromatography column model] | Parameter [Chromatography guard column model] | Parameter [mobile phase] | Parameter [Chromatography injection volume] | Unit | Parameter [Chromatography injection mode] | Parameter [Chromatography gradient] | Sample Name | +|:--------------|:-----------------------------|:----------------------------------------------|:-----------------------------------------------|:-----------------------------------------|:------------------------------------------|:------------------------------------------------|:---------------------------|----------------------------------------------:|:-----------|:--------------------------------------------|:--------------------------------------|--------------:| +| Std. Mix 5µM | | 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 | | 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 | | 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 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-436 | - | helium(0) | 1 | microliter | split | gradient elution | 150112_16 | +| DB23 | 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 | 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 | 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 | 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 | 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 | 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 | | 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 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-444 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_04 | +| DB39 | 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 | 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 | 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 | 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 | 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 | 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 | | 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 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-452 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_26 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/04_metabolites_massspec.md b/_isa-md/assays/GCqTOF_targets/isa.assay/04_metabolites_massspec.md new file mode 100644 index 0000000000000000000000000000000000000000..b8fbf5b50434a294cb6887f0bb564c7900d877ce --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/04_metabolites_massspec.md @@ -0,0 +1,22 @@ +| Source Name | 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 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_03.D | +| 150112_04 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_04.D | +| 150112_15 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_15.D | +| 150112_16 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_16.D | +| 150112_55 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_55.D | +| 150112_56 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_56.D | +| 150112_61 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_61.D | +| 150112_62 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_62.D | +| 150112_65 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_65.D | +| 150112_66 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_66.D | +| 150115_03 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_03.D | +| 150115_04 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_04.D | +| 150115_11 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_11.D | +| 150115_12 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_12.D | +| 150115_13 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_13.D | +| 150115_14 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_14.D | +| 150115_15 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_15.D | +| 150115_16 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_16.D | +| 150115_25 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_25.D | +| 150115_26 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_26.D | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md b/_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md new file mode 100644 index 0000000000000000000000000000000000000000..11481b14f175d510670a32720be8a87efb324829 --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md @@ -0,0 +1,6 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/assays/MassHunter_targets/isa.assay/05_metabolites_datatrans.md b/_isa-md/assays/MassHunter_targets/isa.assay/05_metabolites_datatrans.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/_isa-md/assays/MassHunter_targets/isa.assay/06_metabolites_identification.md b/_isa-md/assays/MassHunter_targets/isa.assay/06_metabolites_identification.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/_isa-md/assays/MassHunter_targets/isa.assay/Assay.md b/_isa-md/assays/MassHunter_targets/isa.assay/Assay.md new file mode 100644 index 0000000000000000000000000000000000000000..9c512c21de6a780f4b164f7bc3437830f3ded7c3 --- /dev/null +++ b/_isa-md/assays/MassHunter_targets/isa.assay/Assay.md @@ -0,0 +1,3 @@ +| ASSAY METADATA | Unnamed: 1 | +|:-----------------|:----------------------------------| +| File Name | MassHunter_targets/isa.assay.xlsx | \ No newline at end of file diff --git a/_isa-md/assays/MassHunter_targets/isa.datapackage/Derivations.md b/_isa-md/assays/MassHunter_targets/isa.datapackage/Derivations.md new file mode 100644 index 0000000000000000000000000000000000000000..6eee651b791e699c9332987258af80e62ed6c693 --- /dev/null +++ b/_isa-md/assays/MassHunter_targets/isa.datapackage/Derivations.md @@ -0,0 +1,25 @@ +| 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 | | | \ No newline at end of file diff --git a/_isa-md/assays/MassHunter_targets/isa.datapackage/Dictionary.md b/_isa-md/assays/MassHunter_targets/isa.datapackage/Dictionary.md new file mode 100644 index 0000000000000000000000000000000000000000..f0cc0f24c6b1051591dfd19330e86b000bce5726 --- /dev/null +++ b/_isa-md/assays/MassHunter_targets/isa.datapackage/Dictionary.md @@ -0,0 +1,26 @@ +| 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 | | | | \ No newline at end of file diff --git a/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/Assay.md b/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/Assay.md new file mode 100644 index 0000000000000000000000000000000000000000..73eba7b7cfdbbaa77ed5b99ed24f131460f4e63a --- /dev/null +++ b/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/Assay.md @@ -0,0 +1,19 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/illumina.md b/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/illumina.md new file mode 100644 index 0000000000000000000000000000000000000000..4296ee396fa53821bb25e4c103a31b3fd2e85285 --- /dev/null +++ b/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/illumina.md @@ -0,0 +1,8 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/rna_extraction.md b/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/rna_extraction.md new file mode 100644 index 0000000000000000000000000000000000000000..de23c8d130506ce61442276a58339156c44c7ad9 --- /dev/null +++ b/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/rna_extraction.md @@ -0,0 +1,8 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/isa.investigation/isa_investigation.md b/_isa-md/isa.investigation/isa_investigation.md new file mode 100644 index 0000000000000000000000000000000000000000..e8d4c84bab975b1dce1e39cfd555200dc9971401 --- /dev/null +++ b/_isa-md/isa.investigation/isa_investigation.md @@ -0,0 +1,73 @@ +| ONTOLOGY SOURCE REFERENCE | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | +|:---------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------|:--------------| +| Term Source Name | PECO | UO | NFDI4PSO | | | | | | | | | | +| Term Source File | http://purl.obolibrary.org/obo/peco.owl | http://purl.obolibrary.org/obo/uo.owl | https://github.com/nfdi4plants/nfdi4plants_ontology/blob/main/nfdi4plants_ontology.obo | | | | | | | | | | +| Term Source Version | releases/2020-08-21 | releases/2020-03-10 | | | | | | | | | | | +| Term Source Description | Plant Experimental Conditions Ontology | Unit ontology | NFDI for Plant Science Ontology | | | | | | | | | | +| Investigation Identifier | samplearc_rnaseq | | | | | | | | | | | | +| Investigation Title | Facultative CAM in Talinum triangulare | | | | | | | | | | | | +| Investigation Submission Date | July 07, 2015 | | | | | | | | | | | | +| Investigation Public Release Date | Nov 05, 2015 | | | | | | | | | | | | +| Investigation Publication PubMed ID | 26530316 | | | | | | | | | | | | +| Investigation Publication DOI | 10.1104/pp.15.01076 | | | | | | | | | | | | +| Investigation Publication Author List | Brilhaus, Dominik; Bräutigam, Andrea; Mettler-Altmann, Tabea; Winter, Klaus; Weber, Andreas P M | | | | | | | | | | | | +| Investigation Publication Title | Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare. | | | | | | | | | | | | +| Investigation Publication Status | Published | | | | | | | | | | | | +| Investigation Person Last Name | Brilhaus | Bräutigam | Mettler-Altmann | Winter | Weber | | | | | | | | +| Investigation Person First Name | Dominik | Andrea | Tabea | Klaus | Andreas | | | | | | | | +| Investigation Person Mid Initials | | | | | P M | | | | | | | | +| Investigation Person Email | dominik.brilhaus@hhu.de | | | | | | | | | | | | +| Investigation Person Phone | 0211-8115523 | | | | | | | | | | | | +| Investigation Person Address | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Universitätsstr. 1, 40225 Düsseldorf | Universitätsstr. 1, 40225 Düsseldorf | Balboa, Ancón, Republic of Panama | Universitätsstr. 1, 40225 Düsseldorf | | | | | | | | +| Investigation Person Affiliation | Institute of Plant Biochemistry, HHU Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | Smithsonian Tropical Research Institute, Panama | Institute of Plant Biochemistry, HHU Düsseldorf | | | | | | | | +| Investigation Person Roles | research assistant | research assistant | research assistant | co-investigator | principal investigator | | | | | | | | +| Investigation 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/co-investigator | http://purl.org/spar/scoro/principal-investigator | | | | | | | | +| Investigation Person Roles Term Source REF | scoro | scoro | scoro | scoro | scoro | | | | | | | | +| Comment[<Investigation Person ORCID>] | http://orcid.org/0000-0001-9021-3197 | http://orcid.org/0000-0002-5309-0527 | http://orcid.org/0000-0002-9161-4889 | | http://orcid.org/0000-0003-0970-4672 | | | | | | | | +| Study Identifier | TalinumFacultativeCAM | | | | | | | | | | | | +| Study File Name | TalinumFacultativeCAM/isa.study.xlsx | | | | | | | | | | | | +| Study Factor Name | watering exposure | Timepoint | timepoint-ZT | Photosynthesis mode | | | | | | | | | +| Study Factor Type | watering exposure | Timepoint | timepoint-ZT | Photosynthesis mode | | | | | | | | | +| Study Factor Type Term Accession Number | http://purl.obolibrary.org/obo/PECO_0007383 | http://purl.obolibrary.org/obo/NCIT_C68568 | | | | | | | | | | | +| Study Factor Type Term Source REF | PECO | NCIT | | | | | | | | | | | +| Study Assay Measurement Type | mRNA Sequencing | GCqTOF targeted | | | | | | | | | | | +| Study Assay Measurement Type Term Accession Number | http://purl.obolibrary.org/obo/NCIT_C129432 | | | | | | | | | | | | +| Study Assay Measurement Type Term Source REF | NCIT | | | | | | | | | | | | +| Study Assay Technology Type | Next Generation Sequencing | | | | | | | | | | | | +| Study Assay Technology Type Term Accession Number | http://purl.obolibrary.org/obo/NCIT_C101293 | | | | | | | | | | | | +| Study Assay Technology Type Term Source REF | NCIT | | | | | | | | | | | | +| Study Assay Technology Platform | Illumina HiSeq 2500 | | | | | | | | | | | | +| Study Assay File Name | Talinum_RNASeq_minimal/isa.assay.xlsx | GCqTOF_targets/isa.assay.xlsx | MassHunter_targets/isa.assay.xlsx | | | | | | | | | | +| Study Protocol Name | rna_extraction | illumina | plant_material.md | rna_extraction.md | illumina.md | 02_metabolites_extr | 03_metabolites_chromatography | 04_metabolites_massspec | 05_metabolites_datatrans | 06_metabolites_identification | | | +| Study Protocol Type | | | plant growth protocol | RNA extraction protocol | assay protocol | | | | | | | | +| Study Protocol Type Term Accession Number | | | http://purl.obolibrary.org/obo/DPBO_1000164 | http://purl.obolibrary.org/obo/DPBO_1000173 | http://purl.obolibrary.org/obo/DPBO_1000177 | | | | | | | | +| Study Protocol Type Term Source REF | | | DPBO | DPBO | DPBO | | | | | | | | +| Study Protocol Parameters Name | biosource amount;extraction method;extraction buffer;extraction buffer volume;RNA quality check | library strategy;library selection;library layout;library preparation kit;library preparation kit version;adapter sequence;next generation sequencing instrument model;base-calling software;base-calling software version;Raw data file format | growth day length;light intensity exposure;humidity day;temperature day;temperature night | biosource amount;extraction method;extraction buffer;extraction buffer volume;RNA quality check | library strategy;library selection;library layout;library preparation kit;library preparation kit version;adapter sequence;next generation sequencing instrument model;base-calling software;base-calling software version;Raw data file format | Bio entity;Biosource amount;Biosource material state;Extraction buffer;Extraction buffer volume;Internal standard;Sample volume;MS sample post-extraction;MS sample resuspension;MS derivatization;label | MS sample type;Chromatography instrument model;Chromatography autosampler model;Chromatography column type;Chromatography column model;Chromatography guard column model;mobile phase;Chromatography injection volume;Chromatography injection mode;Chromatography gradient | scan polarity;scan window lower limit;scan window upper limit;scan rate;instrument model;ionization type;mass analyzer type;detector type | area normalization;data transformation;Metabolite Assignment File;Processed data file format | area normalization;data transformation;Metabolite Assignment File;Processed data file format | | | +| Study Protocol Parameters Term Accession Number | http://purl.obolibrary.org/obo/DPBO_0000013;http://purl.obolibrary.org/obo/DPBO_0000054;http://purl.obolibrary.org/obo/DPBO_0000050;http://purl.obolibrary.org/obo/DPBO_0000051;http://purl.obolibrary.org/obo/DPBO_0000062 | http://purl.obolibrary.org/obo/DPBO_0000035;http://purl.obolibrary.org/obo/DPBO_0000036;http://purl.obolibrary.org/obo/DPBO_0000015;http://purl.obolibrary.org/obo/GENEPIO_0000085;http://purl.obolibrary.org/obo/GENEPIO_0000149;http://purl.obolibrary.org/obo/GENEPIO_0000083;http://purl.obolibrary.org/obo/DPBO_0000040;http://purl.obolibrary.org/obo/DPBO_0000017;http://purl.obolibrary.org/obo/DPBO_0000018;http://purl.obolibrary.org/obo/DPBO_0000021 | http://purl.obolibrary.org/obo/DPBO_0000041;http://purl.obolibrary.org/obo/PECO_0007224;http://purl.obolibrary.org/obo/DPBO_0000005;http://purl.obolibrary.org/obo/DPBO_0000007;http://purl.obolibrary.org/obo/DPBO_0000008 | http://purl.obolibrary.org/obo/DPBO_0000013;http://purl.obolibrary.org/obo/DPBO_0000054;http://purl.obolibrary.org/obo/DPBO_0000050;http://purl.obolibrary.org/obo/DPBO_0000051;http://purl.obolibrary.org/obo/DPBO_0000062 | http://purl.obolibrary.org/obo/DPBO_0000035;http://purl.obolibrary.org/obo/DPBO_0000036;http://purl.obolibrary.org/obo/DPBO_0000015;http://purl.obolibrary.org/obo/GENEPIO_0000085;http://purl.obolibrary.org/obo/GENEPIO_0000149;http://purl.obolibrary.org/obo/GENEPIO_0000083;http://purl.obolibrary.org/obo/DPBO_0000040;http://purl.obolibrary.org/obo/DPBO_0000017;http://purl.obolibrary.org/obo/DPBO_0000018;http://purl.obolibrary.org/obo/DPBO_0000021 | http://purl.obolibrary.org/obo/NFDI4PSO_0000012;http://purl.obolibrary.org/obo/NFDI4PSO_0000013;http://purl.obolibrary.org/obo/NFDI4PSO_0010009;http://purl.obolibrary.org/obo/NFDI4PSO_0000050;http://purl.obolibrary.org/obo/NFDI4PSO_0000051;http://purl.obolibrary.org/obo/NFDI4PSO_0010012;http://purl.obolibrary.org/obo/NFDI4PSO_0010013;http://purl.obolibrary.org/obo/NFDI4PSO_0000043;http://purl.obolibrary.org/obo/NFDI4PSO_0000044;http://purl.obolibrary.org/obo/NFDI4PSO_0000052;http://purl.obolibrary.org/obo/NFDI4PSO_0000079 | http://purl.obolibrary.org/obo/NFDI4PSO_0000045;http://purl.obolibrary.org/obo/NFDI4PSO_0000046;http://purl.obolibrary.org/obo/NFDI4PSO_0000047;http://purl.obolibrary.org/obo/NFDI4PSO_0000053;http://purl.obolibrary.org/obo/NFDI4PSO_0000048;http://purl.obolibrary.org/obo/NFDI4PSO_0000049;http://purl.obolibrary.org/obo/NFDI4PSO_0000080;http://purl.obolibrary.org/obo/NFDI4PSO_0010014;http://purl.obolibrary.org/obo/NFDI4PSO_0010015;http://purl.obolibrary.org/obo/NFDI4PSO_0000081 | http://purl.obolibrary.org/obo/MS_1000465;http://purl.obolibrary.org/obo/MS_1000501;http://purl.obolibrary.org/obo/MS_1000500;http://purl.obolibrary.org/obo/MS_1000015;http://purl.obolibrary.org/obo/MS_1000031;http://purl.obolibrary.org/obo/MS_1000008;http://purl.obolibrary.org/obo/MS_1000443;http://purl.obolibrary.org/obo/MS_1000026 | http://purl.obolibrary.org/obo/MS_1001999;http://purl.obolibrary.org/obo/MS_1000452;http://purl.obolibrary.org/obo/NFDI4PSO_0000077;http://purl.obolibrary.org/obo/NFDI4PSO_0000027 | http://purl.obolibrary.org/obo/MS_1001999;http://purl.obolibrary.org/obo/MS_1000452;http://purl.obolibrary.org/obo/NFDI4PSO_0000077;http://purl.obolibrary.org/obo/NFDI4PSO_0000027 | | | +| Study Protocol Parameters Term Source REF | DPBO;DPBO;DPBO;DPBO;DPBO | DPBO;DPBO;DPBO;GENEPIO;GENEPIO;GENEPIO;DPBO;DPBO;DPBO;DPBO | DPBO;PECO;DPBO;DPBO;DPBO | DPBO;DPBO;DPBO;DPBO;DPBO | DPBO;DPBO;DPBO;GENEPIO;GENEPIO;GENEPIO;DPBO;DPBO;DPBO;DPBO | NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO | NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO;NFDI4PSO | MS;MS;MS;MS;MS;MS;MS;MS | MS;MS;NFDI4PSO;NFDI4PSO | MS;MS;NFDI4PSO;NFDI4PSO | | | +| Comment[<RowRange>] | | | 0:5 | 0:5 | 0:5 | 0:5 | 0:19 | 0:19 | 0:0 | 0:0 | | | +| Study Person Last Name | Brilhaus | Winter | Kurz | Wachtmeister | | Brilhaus | Winter | Brilhaus | Mettler-Altmann | Klemp | Graf | Weber | +| Study Person First Name | Dominik | Klaus | Samantha | Thorsten | | Dominik | Klaus | Dominik | Tabea | Elisabeth | Maria | Katrin | +| Study Person Email | dominik.brilhaus@hhu.de | | | | | dominik.brilhaus@hhu.de | | | | | | | +| Study Person Phone | 0211-8115523 | | | | | 0211-8115523 | | | | | | | +| Study Person Address | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Balboa, Ancón, Republic of Panama | Universitätsstr. 1, 40225 Düsseldorf | Universitätsstr. 1, 40225 Düsseldorf | | 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 | Institute of Plant Biochemistry, HHU Düsseldorf | Biological Medical Research Centre, HHU Düsseldorf | | Institute of Plant Biochemistry, HHU Düsseldorf | Smithsonian Tropical Research Institute, Panama | | | | | | +| Study Person Roles | research assistant | co-investigator | technician | technician | | research assistant | co-investigator | | | | | | +| Study Person 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 | | http://purl.org/spar/scoro/research-assistant | http://purl.org/spar/scoro/co-investigator | | | | | | +| Study Person Roles Term Source REF | scoro | scoro | scoro | scoro | | scoro | scoro | | | | | | +| Comment[<Study Person ORCID>] | | | | | | http://orcid.org/0000-0001-9021-3197 | | | | | | | +| Study Identifier | TalinumGenomeDraft | | | | | | | | | | | | +| Study File Name | TalinumGenomeDraft/isa.study.xlsx | | | | | | | | | | | | +| Study Protocol Name | TalinumGenomeDraft | | | | | | | | | | | | +| Comment[<RowRange>] | 0:0 | | | | | | | | | | | | +| 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 | | | | | | | | | \ No newline at end of file diff --git a/_isa-md/runs/kallisto_collect/out/isa.dataset/Dictionary.md b/_isa-md/runs/kallisto_collect/out/isa.dataset/Dictionary.md new file mode 100644 index 0000000000000000000000000000000000000000..d2c2a934a14242e35ce5c4232f2f21bc8d33ae1b --- /dev/null +++ b/_isa-md/runs/kallisto_collect/out/isa.dataset/Dictionary.md @@ -0,0 +1,14 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/runs/kallisto_sleuth/isa.dataset/Dictionary.md b/_isa-md/runs/kallisto_sleuth/isa.dataset/Dictionary.md new file mode 100644 index 0000000000000000000000000000000000000000..d9e464d12e6238a8bd6c1649e28f3ec20df8b022 --- /dev/null +++ b/_isa-md/runs/kallisto_sleuth/isa.dataset/Dictionary.md @@ -0,0 +1,14 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/studies/TalinumFacultativeCAM/isa.study/Study.md b/_isa-md/studies/TalinumFacultativeCAM/isa.study/Study.md new file mode 100644 index 0000000000000000000000000000000000000000..226516dccf8e08e71c92e0eb09cb42176461d8dd --- /dev/null +++ b/_isa-md/studies/TalinumFacultativeCAM/isa.study/Study.md @@ -0,0 +1,14 @@ +| 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 | | \ No newline at end of file diff --git a/_isa-md/studies/TalinumFacultativeCAM/isa.study/plant_material.md b/_isa-md/studies/TalinumFacultativeCAM/isa.study/plant_material.md new file mode 100644 index 0000000000000000000000000000000000000000..97e5515c16b3010c2faeb3dd18f5b49662a85166 --- /dev/null +++ b/_isa-md/studies/TalinumFacultativeCAM/isa.study/plant_material.md @@ -0,0 +1,8 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/studies/TalinumGenomeDraft/isa.study/Study.md b/_isa-md/studies/TalinumGenomeDraft/isa.study/Study.md new file mode 100644 index 0000000000000000000000000000000000000000..bfdc69daadbb5badc6b55711685fa5639abbef04 --- /dev/null +++ b/_isa-md/studies/TalinumGenomeDraft/isa.study/Study.md @@ -0,0 +1,15 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/studies/TalinumGenomeDraft/isa.study/TalinumGenomeDraft.md b/_isa-md/studies/TalinumGenomeDraft/isa.study/TalinumGenomeDraft.md new file mode 100644 index 0000000000000000000000000000000000000000..fd5a8245d4ae7c02f4443f62a58388aae61cab48 --- /dev/null +++ b/_isa-md/studies/TalinumGenomeDraft/isa.study/TalinumGenomeDraft.md @@ -0,0 +1,3 @@ +| Source Name | Derived Data File | +|:------------------------|:---------------------| +| VariousTalinumData[WIP] | Talinum.gm.CDS.nt.fa | \ No newline at end of file