.arc/validation_packages.yml

-validation_packages:
-    -
-      name: invenio
-      version: 2.0.1
\ No newline at end of file
+arc_specification: 2.0.0-draft
+validation_packages:
+  - name: invenio
+    version: 2.1.0
+  - name: pride
+    version: 1.0.3

README.md

@@ -3,7 +3,7 @@
 [![DOI](https://archive.nfdi4plants.org/badge/DOI/10.60534/9e5jx-75d83.svg)](https://doi.org/10.60534/9e5jx-75d83)
 
 ## Experimental design
-<img src="https://git.nfdi4plants.org/venn/Ru_ChlamyHeatstress/-/raw/main/studies/HeatstressExperiment/protocols/2022-07-12_121059.png" alt="Overview_HS40" width="70%"/>
+<img src="https://git.nfdi4plants.org/venn/Ru_ChlamyHeatstress/-/raw/main/studies/Growth/protocols/2022-07-12_121059.png" alt="Overview_HS40" width="70%"/>
 
 **Figure 1:** Experimental design of the heat treatment experiments (Zhang et al. 2022).
 

runs/Proteomics/run.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+  DockerRequirement:
+    dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: ProteomicsStatistics.fsx
+        entry:
+          $include: ProteomicsStatistics.fsx
+  - class: EnvVarRequirement
+    envDef:
+      - envName: DOTNET_NOLOGO
+        envValue: "true"
+  - class: NetworkAccess
+    networkAccess: true
+baseCommand: [dotnet, fsi, ProteomicsStatistics.fsx]
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: "imputeKnnNoLow_35.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "imputeKnnNoLow_40.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "protein35zScores.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "protein40zScores.txt"
+
+
+arc:has technology type:
+  - class: arc:technology type
+    arc:annotation value: "Docker Container"
+
+arc:technology platform: ".NET"
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Benedikt"
+    arc:last name: "Venn"
+    arc:email: "venn@bio.uni-kl.de"
+    arc:affiliation: "TU Kaiserslautern"
+    arc:has role: 
+      - class: arc:role
+        arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+        arc:annotation value: "Formal analysis"
+
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs10_dep.txt

+redox	18	0.046572
+major CHO metabolism.degradation.starch.starch cleavage	4	0.036255
+TCA / organic transformation.TCA.pyruvate DH	4	0.027340
+secondary metabolism	18	0.023703
+protein.targeting.chloroplast	7	0.021577
+protein.assembly and cofactor ligation	6	0.019517
+amino acid metabolism.synthesis.glutamate family.arginine	5	0.017260
+redox.misc	5	0.017260
+protein.aa activation	14	0.016326
+signalling.phosphinositides.phosphatidylinositol-4-phosphate 5-kinase	4	0.016168
+cell.cycle.peptidylprolyl isomerase	9	0.012316
+cell.motility.eukaryotes.flagellar membrane proteins	4	0.010644
+nucleotide metabolism.phosphotransfer and pyrophosphatases.adenylate kinase	4	0.010644
+PS.calvin cycle.rubisco interacting	4	0.010644
+OPP	6	0.010644
+lipid metabolism	32	0.005106
+PS.lightreaction.other electron carrier (ox/red)	5	0.005099
+PS.lightreaction.unspecified	10	0.004672
+protein.synthesis	48	0.003846
+secondary metabolism.isoprenoids.carotenoids	8	0.002788
+PS.lightreaction.photosystem II.biogenesis	7	0.002023
+PS.lightreaction.cytochrome b6/f	4	0.002010
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex A	4	0.002010
+secondary metabolism.isoprenoids.non-mevalonate pathway	6	0.001055
+protein.folding.immunophilins (IMM)	13	0.000788
+protein.folding.immunophilins (IMM).FKBPs	8	0.000708
+tetrapyrrole synthesis.glu-tRNA synthetase	5	0.000649
+tetrapyrrole synthesis.magnesium chelatase	4	0.000460
+cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species	8	0.000346
+secondary metabolism.isoprenoids	16	0.000262
+lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation	6	0.000190
+cell.motility.eukaryotes.central pair	8	0.000051
+PS.lightreaction.ATP synthase	6	0.000031
+PS.lightreaction.photosystem II.LHC-II	8	0.000014
+nucleotide metabolism.phosphotransfer and pyrophosphatases	11	0.000013
+cell.motility.eukaryotes.radial spoke	9	0.000004
+cell.motility.eukaryotes.radial spoke.stalk	8	0.000003
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar	8	0.000003
+cell.motility.eukaryotes.axonemal dyneins.outer arm	10	0.000001
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit	8	0.000000
+PS.lightreaction.photosystem I.LHC-I	9	0.000000
+PS.lightreaction.photosystem II.PSII polypeptide subunits	12	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit	10	0.000000
+lipid metabolism.FA synthesis and FA elongation	22	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm	16	0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B	10	0.000000
+cell.motility.eukaryotes.flagellar associated proteins	31	0.000000
+PS.lightreaction	77	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit	18	0.000000
+protein.synthesis.ribosomal protein	42	0.000000
+cell.motility.eukaryotes.intraflagellar transport	17	0.000000
+PS.lightreaction.photosystem I.PSI polypeptide subunits	9	0.000000
+PS.lightreaction.photosystem II	28	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast	28	0.000000
+cell.motility.eukaryotes	103	0.000000
+cell.motility	103	0.000000
+cell	129	0.000000
+protein.synthesis.ribosomal protein.prokaryotic	38	0.000000
+PS	104	0.000000
+cell.motility.eukaryotes.axonemal dyneins	26	-0.000000
+PS.lightreaction.photosystem I	18	-0.000000
+tetrapyrrole synthesis	30	-0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein	14	-0.000000
+PS.calvin cycle	16	-0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs10_enr.txt

+secondary metabolism.flavonoids	14	0.042154
+protein.synthesis.ribosome biogenesis.export from nucleus	10	0.038462
+Co-factor and vitamine metabolism.molybdenum cofactor	10	0.038462
+protein.targeting.nucleus	17	0.033204
+DNA	293	0.027849
+protein.degradation.AAA type	15	0.025280
+RNA.regulation of transcription.C2H2 zinc finger family	9	0.025280
+amino acid metabolism.synthesis.histidine	11	0.021176
+protein.degradation.ubiquitin.ubiquitin	17	0.017713
+cell.organisation.cytoskeleton	18	0.009704
+RNA.regulation of transcription.chromatin remodeling factors	30	0.009532
+RNA.processing.RNA helicase	31	0.005939
+protein.degradation.ubiquitin.ubiquitin protease	19	0.005587
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.misc	9	0.004985
+protein.degradation.autophagy	9	0.004985
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.DExD-box helicases	14	0.002698
+protein.synthesis.initiation	40	0.001254
+protein.targeting.secretory pathway.unspecified	38	0.001144
+RNA.processing.ribonucleases	26	0.001061
+misc.UDP glucosyl and glucoronyl transferases	35	0.000955
+cell.organisation	116	0.000570
+misc	216	0.000406
+protein.degradation.ubiquitin.E3.RING	55	0.000375
+protein.degradation.ubiquitin.E2	21	0.000257
+RNA.regulation of transcription.unclassified	65	0.000128
+protein	1150	0.000128
+cell.vesicle transport	47	0.000095
+protein.degradation.ubiquitin.E3	79	0.000075
+DNA.repair	63	0.000056
+RNA.processing	150	0.000056
+protein.targeting	117	0.000005
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications	43	0.000004
+signalling.G-proteins	60	0.000003
+minor CHO metabolism.others	100	0.000001
+protein.targeting.secretory pathway	69	0.000000
+RNA.regulation of transcription	319	0.000000
+DNA.unspecified	45	0.000000
+RNA.transcription	43	0.000000
+cell.division	69	0.000000
+protein.degradation.ubiquitin	219	0.000000
+RNA	553	0.000000
+protein.degradation	408	0.000000
+protein.synthesis.ribosome biogenesis	76	0.000000
+protein.degradation.ubiquitin.proteasom	50	-0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs11_dep.txt

+cell.motility.eukaryotes.flagellar associated proteins	8	0.047242
+glycolysis	6	0.038987
+biodegradation of xenobiotics	4	0.038279
+TCA / organic transformation.TCA	4	0.032588
+major CHO metabolism	8	0.030197
+cell.cycle.peptidylprolyl isomerase	5	0.026293
+protein.folding.immunophilins (IMM)	6	0.018290
+major CHO metabolism.synthesis.starch	4	0.018290
+TCA / organic transformation	6	0.017901
+PS.lightreaction.photosystem II.PSII polypeptide subunits	4	0.010938
+PS.carbon concentrating mechanism	7	0.003636
+TCA / organic transformation.TCA.pyruvate DH	4	0.002073
+PS.lightreaction.unspecified	7	0.001713
+gluconeogenesis / glyoxylate cycle	5	0.000134
+lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation	5	0.000052
+tetrapyrrole synthesis	10	0.000052
+lipid metabolism	27	0.000000
+PS.lightreaction.photosystem II.LHC-II	8	0.000000
+PS.lightreaction.photosystem II	14	0.000000
+PS.lightreaction.photosystem I.PSI polypeptide subunits	7	0.000000
+PS.calvin cycle	11	0.000000
+PS.lightreaction	46	0.000000
+PS.lightreaction.photosystem I.LHC-I	9	0.000000
+PS	65	0.000000
+PS.lightreaction.photosystem I	16	-0.000000
+lipid metabolism.FA synthesis and FA elongation	17	-0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs11_enr.txt

+RNA.RNA binding	53	0.037413
+cell.motility.eukaryotes.basal bodies	23	0.035278
+protein.degradation.ubiquitin.ubiquitin protease	18	0.035154
+RNA.regulation of transcription.C2H2 zinc finger family	9	0.033586
+hormone metabolism.auxin	17	0.030284
+protein.degradation.ubiquitin.ubiquitin	17	0.030284
+hormone metabolism.abscisic acid.signal transduction	7	0.030284
+amino acid metabolism.synthesis.histidine	11	0.030284
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.DExD-box helicases	13	0.025765
+cell.organisation.cytoskeleton.mikrotubuli	13	0.025765
+protein.targeting.secretory pathway.vacuole	13	0.025765
+transport	293	0.020565
+protein.targeting.nucleus	18	0.020534
+protein.targeting.secretory pathway.golgi	10	0.019825
+protein.targeting.secretory pathway.ER	11	0.009532
+RNA.processing.ribonucleases	25	0.009464
+misc.UDP glucosyl and glucoronyl transferases	34	0.008716
+protein.degradation.autophagy	9	0.007633
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.misc	9	0.007633
+RNA.regulation of transcription.putative transcription regulator	36	0.006608
+protein	1197	0.004319
+transport.misc	61	0.004176
+cell.organisation.cytoskeleton	20	0.001113
+development.unspecified	107	0.001019
+cell	407	0.000880
+protein.synthesis.initiation	42	0.000865
+development	120	0.000849
+protein.degradation.ubiquitin.E2	21	0.000678
+RNA.regulation of transcription.unclassified	66	0.000523
+RNA.processing.RNA helicase	35	0.000297
+DNA.repair	64	0.000193
+DNA	329	0.000165
+protein.degradation.ubiquitin.E3.RING	59	0.000078
+RNA.regulation of transcription.chromatin remodeling factors	36	0.000035
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications	43	0.000021
+DNA.unspecified	43	0.000009
+protein.degradation.ubiquitin.E3	86	0.000003
+protein.targeting	125	0.000001
+minor CHO metabolism.others	105	0.000001
+cell.organisation	133	0.000000
+signalling.G-proteins	64	0.000000
+cell.division	69	0.000000
+protein.targeting.secretory pathway.unspecified	47	0.000000
+RNA.transcription	44	0.000000
+protein.synthesis.ribosome biogenesis	77	0.000000
+RNA.regulation of transcription	374	0.000000
+protein.degradation.ubiquitin	223	0.000000
+RNA	650	0.000000
+protein.degradation	403	0.000000
+cell.vesicle transport	57	0.000000
+RNA.processing	179	0.000000
+protein.targeting.secretory pathway	84	0.000000
+protein.degradation.ubiquitin.proteasom	48	0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs12_dep.txt

+amino acid metabolism.degradation	4	0.017144
+lipid metabolism.FA synthesis and FA elongation	4	0.012389
+redox.misc	4	0.000072
+redox	9	0.000057
+fermentation	5	0.000001
+PS.lightreaction.photosystem II	8	0.000001
+PS.lightreaction.hydrogenase.FeFe-hydrogenase	4	0.000000
+PS.lightreaction.hydrogenase	4	0.000000
+PS.lightreaction	15	0.000000
+PS	18	0.000000
+PS.lightreaction.photosystem II.LHC-II	7	0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs12_enr.txt

+protein.synthesis.ribosome biogenesis.BRIX	4	0.045079
+protein	402	0.045079
+RNA.transcription	15	0.040772
+protein.degradation.ubiquitin.E3.RING	22	0.036724
+amino acid metabolism	48	0.023950
+RNA.regulation of transcription.unclassified	26	0.021243
+protein.targeting.secretory pathway.unspecified	17	0.017907
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs	6	0.012753
+RNA.regulation of transcription.C2H2 zinc finger family	6	0.012753
+cell wall.cell wall proteins	5	0.012753
+DNA.synthesis/chromatin structure.histone.core.H2B	11	0.012753
+DNA.synthesis/chromatin structure.histone.core.H2A	18	0.010517
+protein.synthesis.ribosome biogenesis.export from nucleus	7	0.007596
+amino acid metabolism.synthesis	37	0.007323
+RNA.regulation of transcription.SNF7	5	0.005777
+DNA	120	0.005055
+protein.degradation.autophagy	7	0.000676
+protein.synthesis.ribosomal protein	48	0.000343
+amino acid metabolism.synthesis.histidine	9	0.000235
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.misc	8	0.000035
+DNA.synthesis/chromatin structure.histone.core	45	0.000017
+DNA.synthesis/chromatin structure	107	0.000013
+protein.synthesis.ribosomal protein.eukaryotic.60S subunit	29	0.000000
+protein.synthesis.ribosomal protein.eukaryotic	38	0.000000
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications	28	0.000000
+protein.synthesis	122	0.000000
+DNA.synthesis/chromatin structure.histone	85	0.000000
+protein.synthesis.ribosome biogenesis	52	0.000000