diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md b/_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md
deleted file mode 100644
index 11481b14f175d510670a32720be8a87efb324829..0000000000000000000000000000000000000000
--- a/_isa-md/assays/GCqTOF_targets/isa.assay/Assay.md
+++ /dev/null
@@ -1,6 +0,0 @@
-| 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/GCqTOF_targets/isa.assay/gas_chromatography.md b/_isa-md/assays/GCqTOF_targets/isa.assay/gas_chromatography.md
deleted file mode 100644
index 5e7bcfc8e62eac80d11771b1ad315e0c7510b5ef..0000000000000000000000000000000000000000
--- a/_isa-md/assays/GCqTOF_targets/isa.assay/gas_chromatography.md
+++ /dev/null
@@ -1,22 +0,0 @@
-| 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 |
\ No newline at end of file
diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md b/_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md
deleted file mode 100644
index 9ec4346a00050d18196888294bc8650805cd4298..0000000000000000000000000000000000000000
--- a/_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md
+++ /dev/null
@@ -1,22 +0,0 @@
-| 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 |
\ No newline at end of file
diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md b/_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md
deleted file mode 100644
index 2f8c22da2b5aa5207a1c31eefe3423c7e9faf899..0000000000000000000000000000000000000000
--- a/_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md
+++ /dev/null
@@ -1,9 +0,0 @@
-| 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 |
\ 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
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/_isa-md/assays/MassHunter_targets/isa.assay/Assay.md b/_isa-md/assays/MassHunter_targets/isa.assay/Assay.md
deleted file mode 100644
index 9c512c21de6a780f4b164f7bc3437830f3ded7c3..0000000000000000000000000000000000000000
--- a/_isa-md/assays/MassHunter_targets/isa.assay/Assay.md
+++ /dev/null
@@ -1,3 +0,0 @@
-| 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
deleted file mode 100644
index 6eee651b791e699c9332987258af80e62ed6c693..0000000000000000000000000000000000000000
--- a/_isa-md/assays/MassHunter_targets/isa.datapackage/Derivations.md
+++ /dev/null
@@ -1,25 +0,0 @@
-| 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
deleted file mode 100644
index f0cc0f24c6b1051591dfd19330e86b000bce5726..0000000000000000000000000000000000000000
--- a/_isa-md/assays/MassHunter_targets/isa.datapackage/Dictionary.md
+++ /dev/null
@@ -1,26 +0,0 @@
-| 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
deleted file mode 100644
index 73eba7b7cfdbbaa77ed5b99ed24f131460f4e63a..0000000000000000000000000000000000000000
--- a/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/Assay.md
+++ /dev/null
@@ -1,19 +0,0 @@
-| 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
deleted file mode 100644
index 4296ee396fa53821bb25e4c103a31b3fd2e85285..0000000000000000000000000000000000000000
--- a/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/illumina.md
+++ /dev/null
@@ -1,8 +0,0 @@
-| 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
deleted file mode 100644
index de23c8d130506ce61442276a58339156c44c7ad9..0000000000000000000000000000000000000000
--- a/_isa-md/assays/Talinum_RNASeq_minimal/isa.assay/rna_extraction.md
+++ /dev/null
@@ -1,8 +0,0 @@
-| 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
deleted file mode 100644
index e8d4c84bab975b1dce1e39cfd555200dc9971401..0000000000000000000000000000000000000000
--- a/_isa-md/isa.investigation/isa_investigation.md
+++ /dev/null
@@ -1,73 +0,0 @@
-| 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
deleted file mode 100644
index d2c2a934a14242e35ce5c4232f2f21bc8d33ae1b..0000000000000000000000000000000000000000
--- a/_isa-md/runs/kallisto_collect/out/isa.dataset/Dictionary.md
+++ /dev/null
@@ -1,14 +0,0 @@
-| 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
deleted file mode 100644
index d9e464d12e6238a8bd6c1649e28f3ec20df8b022..0000000000000000000000000000000000000000
--- a/_isa-md/runs/kallisto_sleuth/isa.dataset/Dictionary.md
+++ /dev/null
@@ -1,14 +0,0 @@
-| 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
deleted file mode 100644
index 226516dccf8e08e71c92e0eb09cb42176461d8dd..0000000000000000000000000000000000000000
--- a/_isa-md/studies/TalinumFacultativeCAM/isa.study/Study.md
+++ /dev/null
@@ -1,14 +0,0 @@
-| 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
deleted file mode 100644
index 97e5515c16b3010c2faeb3dd18f5b49662a85166..0000000000000000000000000000000000000000
--- a/_isa-md/studies/TalinumFacultativeCAM/isa.study/plant_material.md
+++ /dev/null
@@ -1,8 +0,0 @@
-| 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
deleted file mode 100644
index bfdc69daadbb5badc6b55711685fa5639abbef04..0000000000000000000000000000000000000000
--- a/_isa-md/studies/TalinumGenomeDraft/isa.study/Study.md
+++ /dev/null
@@ -1,15 +0,0 @@
-| 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
deleted file mode 100644
index fd5a8245d4ae7c02f4443f62a58388aae61cab48..0000000000000000000000000000000000000000
--- a/_isa-md/studies/TalinumGenomeDraft/isa.study/TalinumGenomeDraft.md
+++ /dev/null
@@ -1,3 +0,0 @@
-| Source Name | Derived Data File |
-|:------------------------|:---------------------|
-| VariousTalinumData[WIP] | Talinum.gm.CDS.nt.fa |
\ No newline at end of file
diff --git a/_workflow_scheme/README.md b/_workflow_scheme/README.md
deleted file mode 100644
index 79e5ebf37c5aea743071d8e9ead35c167f065022..0000000000000000000000000000000000000000
--- a/_workflow_scheme/README.md
+++ /dev/null
@@ -1,31 +0,0 @@
-
-# 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*
-```
\ No newline at end of file
diff --git a/_workflow_scheme/drawioimport.csv b/_workflow_scheme/drawioimport.csv
deleted file mode 100644
index a78b3fcb1f2a3a97e4b939c7976932a073473c70..0000000000000000000000000000000000000000
--- a/_workflow_scheme/drawioimport.csv
+++ /dev/null
@@ -1,16 +0,0 @@
-step,folder,fill,stroke,shape,id
-assays/Talinum_RNASeq_minimal,assays,#FFC000,#2D3E69,rectangle,1
-runs/shiny_prep,runs,#C21F3A,#2D3E69,ellipse,2
-runs/kallisto_quant,runs,#C21F3A,#2D3E69,ellipse,3
-runs/merged_isa_metadata,runs,#C21F3A,#2D3E69,ellipse,4
-runs/kallisto_collect,runs,#C21F3A,#2D3E69,ellipse,5
-runs/kallisto_index,runs,#C21F3A,#2D3E69,ellipse,6
-runs/kallisto_sleuth,runs,#C21F3A,#2D3E69,ellipse,7
-studies/TalinumGenomeDraft,studies,#B4CE82,#2D3E50,rectangle,8
-studies/TalinumFacultativeCAM,studies,#B4CE82,#2D3E50,rectangle,9
-workflows/merge_isa_metadata,workflows,#4FB3D9,#2D3E57,rhombus,10
-workflows/shiny_prep,workflows,#4FB3D9,#2D3E57,rhombus,11
-workflows/kallisto_quant,workflows,#4FB3D9,#2D3E57,rhombus,12
-workflows/kallisto_collect,workflows,#4FB3D9,#2D3E57,rhombus,13
-workflows/kallisto_index,workflows,#4FB3D9,#2D3E57,rhombus,14
-workflows/kallisto_sleuth,workflows,#4FB3D9,#2D3E57,rhombus,15
diff --git a/_workflow_scheme/drawioimport_header b/_workflow_scheme/drawioimport_header
deleted file mode 100644
index 5365f3e9ec0b5056e21f3853b15ea01dec83e178..0000000000000000000000000000000000000000
--- a/_workflow_scheme/drawioimport_header
+++ /dev/null
@@ -1,13 +0,0 @@
-## Hello World
-# label: %step%
-# style: shape=%shape%;fillColor=%fill%;strokeColor=%stroke%;
-# namespace: csvimport-
-# width: auto
-# height: auto
-# padding: 15
-# ignore: id,shape,fill,stroke,folder
-# nodespacing: 40
-# levelspacing: 100
-# edgespacing: 40
-# layout: auto
-## CSV starts under this line
diff --git a/_workflow_scheme/drawioimport_ready b/_workflow_scheme/drawioimport_ready
deleted file mode 100644
index 206eeca99f364715dd5fefca5497e6853fd03f31..0000000000000000000000000000000000000000
--- a/_workflow_scheme/drawioimport_ready
+++ /dev/null
@@ -1,29 +0,0 @@
-## Hello World
-# label: %step%
-# style: shape=%shape%;fillColor=%fill%;strokeColor=%stroke%;
-# namespace: csvimport-
-# width: auto
-# height: auto
-# padding: 15
-# ignore: id,shape,fill,stroke,folder
-# nodespacing: 40
-# levelspacing: 100
-# edgespacing: 40
-# layout: auto
-## CSV starts under this line
-step,folder,fill,stroke,shape,id
-assays/Talinum_RNASeq_minimal,assays,#FFC000,#2D3E69,rectangle,1
-runs/shiny_prep,runs,#C21F3A,#2D3E69,ellipse,2
-runs/kallisto_quant,runs,#C21F3A,#2D3E69,ellipse,3
-runs/merged_isa_metadata,runs,#C21F3A,#2D3E69,ellipse,4
-runs/kallisto_collect,runs,#C21F3A,#2D3E69,ellipse,5
-runs/kallisto_index,runs,#C21F3A,#2D3E69,ellipse,6
-runs/kallisto_sleuth,runs,#C21F3A,#2D3E69,ellipse,7
-studies/TalinumGenomeDraft,studies,#B4CE82,#2D3E50,rectangle,8
-studies/TalinumFacultativeCAM,studies,#B4CE82,#2D3E50,rectangle,9
-workflows/merge_isa_metadata,workflows,#4FB3D9,#2D3E57,rhombus,10
-workflows/shiny_prep,workflows,#4FB3D9,#2D3E57,rhombus,11
-workflows/kallisto_quant,workflows,#4FB3D9,#2D3E57,rhombus,12
-workflows/kallisto_collect,workflows,#4FB3D9,#2D3E57,rhombus,13
-workflows/kallisto_index,workflows,#4FB3D9,#2D3E57,rhombus,14
-workflows/kallisto_sleuth,workflows,#4FB3D9,#2D3E57,rhombus,15
diff --git a/_workflow_scheme/workflow-scheme.drawio.png b/_workflow_scheme/workflow-scheme.drawio.png
deleted file mode 100644
index d659d714d2dc8035632444eded6d349f71775b88..0000000000000000000000000000000000000000
Binary files a/_workflow_scheme/workflow-scheme.drawio.png and /dev/null differ